[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Expose TLS config on Docker storage ## Opened from the [Prefect Public Slack Community](https://join.slack.com/t/prefect-public/shared_invite/enQtNzE5OTU3OTQwNzc1LTQ5M2FkZmQzZjI0ODg1ZTBmOTc0ZjVjYWFjMWExZDAyYzBmYjVmMTE1NTQ1Y2IxZTllOTc4MmI3NzYxMDlhYWU) **aseev.arsenii**: Hey all! I'm trying to set up a CircleCI job that builds and pushes flows Docker images to AWS ECR. CircleCI provides a remote docker execution environment, and to connect to it I need to pass on TLS configuration to the docker client. Unfortunately Prefect seems to only expose the `base_image` of `docker.APIClient` (<https://github.com/PrefectHQ/prefect/blob/1447982cc63a1f87c4a19cc7be18f2b2693fb883/src/prefect/environments/storage/docker.py#L508>). Any suggestions on how to do this? Thanks! **laura**: Hi <@UR914ST7H>, I’m not sure of a workaround per se but it looks like the signature of exactly where you found the client instantiation could be changed to accept TLS config, configured by the user against an attribute of the `Docker` Storage instance like you can for `base_url` now. Let me get the bot to open an issue off this thread. **laura**: <@ULVA73B9P> open “Expose TLS config on Docker storage” Original thread can be found [here](https://prefect-community.slack.com/archives/CL09KU1K7/p1590055135302100?thread_ts=1590055135.302100&cid=CL09KU1K7). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Search query handles os_build and arch_build as options When searching for the packages of a receipe os_build and arch_build are not take into account correctly. Even if a package matches, it is not included in the resulting list. From what I can see, only specific strings in the query are treated as settings, all others as options. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: PauliFeatureMap docs not formatted correctly <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: master - **Python version**: - **Operating system**: ### What is the current behavior? <img width="803" alt="Screen Shot 2020-05-01 at 09 08 00" src="https://user-images.githubusercontent.com/1249193/80807526-6d60d900-8b8b-11ea-9d29-83cb814f2000.png"> ### Steps to reproduce the problem ### What is the expected behavior? ### Suggested solutions Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: execute gives depreciation warnings <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: master - **Python version**: - **Operating system**: ### What is the current behavior? ```python from qiskit import * sim = Aer.get_backend('unitary_simulator') qr = QuantumRegister(2, name='q') qc = QuantumCircuit(qr) execute(qc, sim); ``` gives ```python /Users/paul/Desktop/Github_repos/qiskit-terra/qiskit/validation/base.py:360: DeprecationWarning: The as_dict() method is deprecated, use to_dict(). DeprecationWarning) /Users/paul/Desktop/Github_repos/qiskit-terra/qiskit/validation/base.py:360: DeprecationWarning: The as_dict() method is deprecated, use to_dict(). DeprecationWarning) ``` ### Steps to reproduce the problem ### What is the expected behavior? ### Suggested solutions Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Create contextmanager for set_dirty/clean_dirty functions Consider creating a `contextmanager` for the `set_dirty/clean_dirty` functions, it may have an optional argument to delete the directory if an exception is raised. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Cloud PR references Core See https://github.com/PrefectHQ/cloud/pull/1394 for more details Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: rename or remove %profile magic This is an issue to discuss what we should do with the `%profile` magic. Background: This magic currently returns the name of the active profile. By name, it is easily confused with the functionality found in `%prun` and `%run -p`. Renaming or removing the current implementation of `%profile` opens up the possibility to use `%profile` for code profiling purposes. Here are a few proposals: (please feel free to add others) 1. Rename `%profile` to `%profile_name` to better signify that it does not do code profiling. 2. Deprecate and then remove `%profile` and tell users to use `get_ipython().profile` rename or remove %profile magic This is an issue to discuss what we should do with the `%profile` magic. Background: This magic currently returns the name of the active profile. By name, it is easily confused with the functionality found in `%prun` and `%run -p`. Renaming or removing the current implementation of `%profile` opens up the possibility to use `%profile` for code profiling purposes. Here are a few proposals: (please feel free to add others) 1. Rename `%profile` to `%profile_name` to better signify that it does not do code profiling. 2. Deprecate and then remove `%profile` and tell users to use `get_ipython().profile` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: RemoteEnvironment doesn't use storage.get_flow() in execute() Basically, this: https://github.com/PrefectHQ/prefect/blob/6fe3fc31ce7023403ef0048e7ea1318501391111/src/prefect/environments/execution/remote.py#L68 I thought that an environment would use storage.get_flow() method to retrieve the flow to ensure universal compatibility of different envs/storages. Not opened as a bug because I'm not sure it is, maybe I'm missing something. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Failure to find linker for custom_target Meson failes to determine linker if multiple languages are used and a custom_target is the sole source file of a shared library: == meson.build == project ('Showcase for custom_target source', ['c', 'cpp']) Foo_cc = custom_target ('Foo.cc', command : [ 'touch', '@OUTPUT@' ], output : 'Foo.cc') Somelib = shared_library ('Somelib', [ Foo_cc ]) == build result == File "/tmp/meson/mesonbuild/backend/backends.py", line 290, in determine_linker raise RuntimeError('Unreachable code') RuntimeError: Unreachable code Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Add MEGA ### Model description MEGA introduces a new attention method which incorporates gating and exponential moving averages to create strong local dependencies, reducing the need for full softmax attention. MEGA set a new SOTA on Long Range Arena, and MEGA-chunk performs nearly as well while achieving linear complexity WRT sequence length. I have seen really promising results from my own experiments with MEGA on long documents -- both in efficiency and model performance. It would be awesome to have MEGA (+ MEGA-chunk) available in the Hugging Face ecosystem! ### Open source status - [X] The model implementation is available - [X] The model weights are available ### Provide useful links for the implementation * [Paper](https://arxiv.org/abs/2209.10655) * [Official implementation](https://github.com/facebookresearch/mega) * [Links to pretrained weights](https://github.com/facebookresearch/mega#models-checkpoints) * I'm only aware of @violet-zct through the official MEGA repo Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: Add support for -H and TLS flags The `docker-compose` command should support these options from the `docker` command: ``` -H, --host=[] Daemon socket(s) to connect to --tls=false Use TLS; implied by --tlsverify --tlscacert=~/.docker/ca.pem Trust certs signed only by this CA --tlscert=~/.docker/cert.pem Path to TLS certificate file --tlskey=~/.docker/key.pem Path to TLS key file --tlsverify=false Use TLS and verify the remote ``` This will allow you to do `docker-compose $(docker-machine config dev) ...` etc. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: [bug] `token` not supported in `AutoModel` I see `use_auth_token` is already deprecated and will be replaced by `token`, https://github.com/huggingface/transformers/blob/b257c46a075419c09e5ce5c5aa39bc346ecdb9a5/src/transformers/modeling_utils.py#L2196-L2204 But `AutoModel` doesn't accept the new argument `token` yet. Especially in https://github.com/huggingface/transformers/blob/b257c46a075419c09e5ce5c5aa39bc346ecdb9a5/src/transformers/configuration_utils.py#L631-L638 Directly call `LlamaForCausalLM` instead of `AutoModelForCausalLM` is a temporary workaround to get rid of the deprecation warning. ### Reproduction ```python3 transformers.AutoModelForCausalLM.from_pretrained('meta-llama/Llama-2-7b-chat-hf',use_auth_token='XXX') transformers.LlamaForCausalLM.from_pretrained('meta-llama/Llama-2-7b-chat-hf',token='XXX') ``` ### Expected behavior `AutoModel` should support new `token` argument. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: More incompatibilities of `TaperedPauliSumOp` <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: master @ 28c543ae - **Python version**: 3.8.8 - **Operating system**: Linux, Fedora 33: `uname -r: 5.11.10-200.fc33.x86_64` ### What is the current behavior? `TaperedPauliSumOp` cannot be multiplied with another `OperatorBase`. ### Steps to reproduce the problem Try the following snippet: ```python from qiskit.circuit import Parameter from qiskit.opflow import PauliSumOp, TwoQubitReduction from qiskit.opflow.evolutions import PauliTrotterEvolution qubit_op = PauliSumOp.from_list([ ("IIII", -0.8105479805373266), ("IIIZ", 0.17218393261915552), ("IIZZ", -0.22575349222402472), ("IZZI", 0.1721839326191556), ("ZZII", -0.22575349222402466), ("IIZI", 0.1209126326177663), ("IZZZ", 0.16892753870087912), ("IXZX", -0.045232799946057854), ("ZXIX", 0.045232799946057854), ("IXIX", 0.045232799946057854), ("ZXZX", -0.045232799946057854), ("ZZIZ", 0.16614543256382414), ("IZIZ", 0.16614543256382414), ("ZZZZ", 0.17464343068300453), ("ZIZI", 0.1209126326177663), ]) tapered_qubit_op = TwoQubitReduction(num_particles=2).convert(qubit_op) param = Parameter('c') param * tapered_qubit_op ``` ### What is the expected behavior? The multiplication should work just fine. ### Suggested solutions Since this is very similar error to #6100 I suggest to find a more general solution which makes `TaperedPauliSumOp` generally compatible. I am quite positive that otherwise more such problems will arise. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: docker-compose run --rm does not remove volumes Running one-off commands with docker-compose does not delete volumes used by the container. This is different than `docker run --rm` which does remove volumes after the container is deleted. docker-compose config --volumes In addition to ``` $ docker-compose config --services ``` it'd be nice to have ``` $ docker-compose config --volumes ``` listing the named volumes similarly to services. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Documentation missing is_decoder ### System Info Not relevant. Issue is about online documentation. ### Who can help? @sgugger @stevhliu ### Information - [ ] The official example scripts - [ ] My own modified scripts ### Tasks - [ ] An officially supported task in the `examples` folder (such as GLUE/SQuAD, ...) - [ ] My own task or dataset (give details below) ### Reproduction The bert documentation [page](https://huggingface.co/docs/transformers/model_doc/bert) mentions `is_decoder` 5 times but the BertConfig [class documentation](https://huggingface.co/docs/transformers/model_doc/bert) not a single time. This probably affects other models as well. ### Expected behavior BertConfig class documentation should contain an entry for `is_decoder`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the celery/celery codebase. Here's the problem: Prepend to sys.path in the Django fixup instead of appending. This makes sure that project modules have precedence over system ones. Closes #5347. ## Description This follows @Phyks's suggestion of a fix for #5347, by prepending instead of appending to the system path, to ensure that the project modules are not hidden by system-wide ones. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: docs: compiler.find_library: discourage lib prefix I continue seeing it in the wild. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: How to use ReduceLROnPlateau methon in matster branch version? #### What is your question? I find the log design has changed a lot between version 0.8.5 and master branch [0c26468](https://github.com/PyTorchLightning/pytorch-lightning/tree/0c264689cb566582ac47333d8b7192d656e19440) I got the error message when I follow the [docs logging-from-a-lightningmodule](https://pytorch-lightning.readthedocs.io/en/latest/loggers.html#logging-from-a-lightningmodule) to modify the log code. error message: ``` MisconfigurationException: ReduceLROnPlateau conditioned on metric val_loss which is not available. Available metrics are: val_early_stop_on,val_checkpoint_on,epoch,checkpoint_on. Condition can be set using `monitor` key in lr scheduler dict ``` #### Code ```python def configure_optimizers(self): optimizer = torch.optim.Adam(self.parameters(), lr = 0.01) scheduler = ReduceLROnPlateau(optimizer, patience=10) return [optimizer], [scheduler] def validation_step(self, batch, batch_nb): x, y = batch y_hat = self(x) loss = F.l1_loss(y, y_hat) result = pl.EvalResult() result.log('val_step_loss', loss) return result def validation_epoch_end(self, outputs): avg_loss = outputs.val_step_loss.mean() result = pl.EvalResult() result.log('val_loss', avg_loss) return result ``` I wonder if I should defined `validation_epoch_end` like above, **if there are any example about how to use `ReduceLROnPlateau` in a right way?** #### What's your environment? - OS: Ubuntu 18.04 - Packaging pip - Version 0.9.0 rc 12 master branch [0c26468](https://github.com/PyTorchLightning/pytorch-lightning/tree/0c264689cb566582ac47333d8b7192d656e19440) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Handle serialization of State results We need to put together a new serializer spec for how to handle state results. An edge case that comes to mind is `Failed` states --> should we be storing the caught exceptions in the DB, or not? We have discussed that you can fail a task and _still_ pass data around (which is 💯 ) and makes me think we should avoid ever storing the `.result` attribute Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: tools.patch cant create files To help us debug your issue please explain: - [x] I've read the [CONTRIBUTING guide](https://github.com/conan-io/conan/blob/develop/.github/CONTRIBUTING.md). - [x] I've specified the Conan version, operating system version and any tool that can be relevant. - [x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Hello, I am trying to apply some out-of-tree git patches, some of them create new files. Some of them contain new files, and the tools.patch utility will then compail that absolute filepaths are not allowed (`/dev/null`). Lacking this support, its cumbersome to add bugfixes and git commits in general. Example patch (created with `git format-patch`): ```patch From d0807313143bb35da65c2b858a2d9e17fd3fbf9e Mon Sep 17 00:00:00 2001 From: Norbert Lange <nolange79@gmail.com> Date: Fri, 7 Jun 2019 21:49:19 +0200 Subject: [PATCH] add and remove file --- newfile | 1 + oldfile | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 newfile delete mode 100644 oldfile diff --git a/newfile b/newfile new file mode 100644 index 0000000..fdedddf --- /dev/null +++ b/newfile @@ -0,0 +1 @@ +Hello mean world diff --git a/oldfile b/oldfile deleted file mode 100644 index 32332e1..0000000 --- a/oldfile +++ /dev/null @@ -1 +0,0 @@ -Old litter -- 2.20.1 ``` My environment is: ``` Debian Buster x64 Conan version 1.16.0 ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: RFC: merging __init__() and run() arguments #291 raises the specter of an old discussion we had tabled -- how to handle arguments that are appropriate for both `__init__` and `run`. In short: flows built with the functional API will prefer run() arguments, since the user often isn't instantiating the task explicitly at all. Conversely, flows built with the imperative API are instantiated and then attached to other tasks explicitly, so __init__() seems more appropriate. If we don't provide some way of doing this, then users will end up writing repetitive code which is unpleasant: ```python class MyTask(Task): def __init__(self, a, b): self.a = a self.b = b def run(self, a=None, b=None): a = self.a if a is None else a b = self.b if b is None else b ``` I'll throw out two possible alternatives to get the ball rolling: - This decorator provides default values for any specified run arguments, retrieving those values from instance attributes of the same name. ```python class MyTask(Task): def __init__(self, a, b): self.a = a self.b = b @defaults_from_attrs('a', 'b') def run(self, a, b): ... ``` This indicates the same thing, but uses Python 3 annotations instead. ```python class MyTask(Task): def __init__(self, a, b): self.a = a self.b = b def run(self, a:DefaultFromAttr, b:DefaultFromAttr): ... ``` The annotations approach has the disadvantage of not allowing proper typing of the argument itself. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: DuplicateTaskIdFound when reusing tasks with task_group decorator ### Apache Airflow version 2.2.2 (latest released) ### Operating System MacOS 11.6.1 ### Versions of Apache Airflow Providers $ pip freeze | grep airflow apache-airflow==2.2.2 apache-airflow-providers-celery==2.1.0 apache-airflow-providers-ftp==2.0.1 apache-airflow-providers-http==2.0.1 apache-airflow-providers-imap==2.0.1 apache-airflow-providers-sqlite==2.0.1 ### Deployment Other ### Deployment details `airflow standalone` ### What happened Exception raised : ``` raise DuplicateTaskIdFound(f"Task id '{key}' has already been added to the DAG") airflow.exceptions.DuplicateTaskIdFound: Task id 'do_all_things.do_thing__1' has already been added to the DAG ``` ### What you expected to happen _No response_ ### How to reproduce * Add the following python file to the `dags` folder: ```python from datetime import datetime from airflow.decorators import dag, task, task_group @dag(start_date=datetime(2023, 1, 1), schedule_interval="@once") def test_dag_1(): @task def start(): pass @task def do_thing(x): print(x) @task_group def do_all_things(): for i in range(5): do_thing(i) @task def end(): pass start() >> do_all_things() >> end() test_dag_1() ``` * Start airflow by running `airflow standalone` ### Anything else _No response_ ### Are you willing to submit PR? - [ ] Yes I am willing to submit a PR! ### Code of Conduct - [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Missing LINK_ARGS -framework for OpenCL run-time dependency tries to link a directory Looks like it's attempting to link a directory instead of referencing the framework: ``` ld: can't map file, errno=22 file '/System/Library/Frameworks/OpenCL.framework' for architecture x86_64 ``` In https://github.com/LeelaChessZero/lc0/issues/972 I bisected meson finding two changes that seemed to change the build.ninja line for LINK_ARGS. 0.51.0: ``` -L/usr/local/opt/openssl/lib -Wl,-dead_strip_dylibs /usr/local/Cellar/protobuf/3.10.0/lib/libprotobuf.dylib -lpthread -F/System/Library/Frameworks -framework Accelerate -F/System/Library/Frameworks -framework OpenCL /usr/lib/libz.dylib -Wl,-headerpad_max_install_names -Wl,-rpath,/usr/local/Cellar/protobuf/3.10.0/lib -Wl,-rpath,/usr/lib ``` (Has `-framework OpenCL`) After https://github.com/mesonbuild/meson/commit/5bd21a96b89efc5fe96025398151dcbce34345ac ``` -L/usr/local/opt/openssl/lib -Wl,-dead_strip_dylibs /usr/local/Cellar/protobuf/3.10.0/lib/libprotobuf.dylib -lpthread -F/System/Library/Frameworks -framework Accelerate /usr/lib/libz.dylib -Wl,-headerpad_max_install_names -Wl,-rpath,/usr/local/Cellar/protobuf/3.10.0/lib -Wl,-rpath,/usr/lib ``` (Removes `-framework OpenCL`) After https://github.com/mesonbuild/meson/commit/f097b96883a54868cf98600be23893268b5832f4 ``` -L/usr/local/opt/openssl/lib -Wl,-dead_strip_dylibs -Wl,-undefined,error -Wl,-headerpad_max_install_names /usr/local/Cellar/protobuf/3.10.0/lib/libprotobuf.dylib -lpthread -F/System/Library/Frameworks -framework Accelerate /System/Library/Frameworks/OpenCL.framework /usr/lib/libz.dylib -Wl,-headerpad_max_install_names -Wl,-rpath,/usr/local/Cellar/protobuf/3.10.0/lib -Wl,-rpath,/usr/lib ``` (Adds `/System/Library/Frameworks/OpenCL.framework`) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Programmatic customization of run_id for scheduled DagRuns ### Description Allow DAG authors to control how `run_id`'s are generated for created DagRuns. Currently the only way to specify a DagRun's `run_id` is through the manual trigger workflow either through the CLI or API and passing in `run_id`. It would be great if DAG authors are able to write a custom logic to generate `run_id`'s from scheduled `DagRunInterval`'s. ### Use case/motivation In Airflow 1.x, the semantics of `execution_date` were burdensome enough for users that DAG authors would subclass DAG to override `create_dagrun` so that when new DagRuns were created, they were created with `run_id`'s that provided context into semantics about the DagRun. For example, ``` def create_dagrun(self, **kwargs): kwargs['run_id'] = kwargs['execution_date'] + self.following_schedule(kwargs['execution_date']).date() return super().create_dagrun(kwargs) ``` would result in the UI DagRun dropdown to display the weekday of when the Dag actually ran. <img width="528" alt="image001" src="https://user-images.githubusercontent.com/9851473/156280393-e261d7fa-dfe0-41db-9887-941510f4070f.png"> After upgrading to Airflow 2.0 and with Dag serialization in the scheduler overridden methods are no longer there in the SerializedDAG, so we are back to having `scheduled__<execution_date>` values in the UI dropdown. It would be great if some functionality could be exposed either through the DAG or just in the UI to display meaningful values in the DagRun dropdown. ### Related issues _No response_ ### Are you willing to submit a PR? - [X] Yes I am willing to submit a PR! ### Code of Conduct - [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the gitpython-developers/GitPython codebase. Here's the problem: Use of GIT_REPO env-var for setting Repo path in 2.0.9 [This change](https://github.com/gitpython-developers/GitPython/commit/26bb778b34b93537cfbfd5c556d3810f2cf3f76e) in `2.0.9` is a bit problematic: - Even if a `path` is explicitly provided to the constructor, the `GIT_DIR` environment variable is used instead - For things like git hooks, `GIT_DIR` is set to `.git` by default. This will result in [`self.git_dir`](https://github.com/gitpython-developers/GitPython/blob/master/git/repo/base.py#L156) being set to `.git` (`os.path.abspath` instead of `os.path.normpath` would fix this). Consequently, subsequent commands fails (eg: `repo.git.status()`) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the explosion/spaCy codebase. Here's the problem: Dummy command argument wasn't removed from auto-link after download Auto-linking of downloaded languages was broken in https://github.com/explosion/spaCy/commit/7f0ab145e95036a55af4802184a4b1c496557d0a. The dummy argument wasn't removed from the `link` call at https://github.com/explosion/spaCy/blob/master/spacy/cli/download.py#L44. I can make a PR for the fix unless it's easier for a maintainer to just fix this quickly. ## Your Environment * Operating System: Docker python:3.6 * Python Version Used: 3.6.2 * spaCy Version Used: Changes made since 2.0.5 * Environment Information: Docker python:3.6 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Sampler fails on gates with unhashable parameters ### Environment - **Qiskit Terra version**: fbff44bfe9ebc9d97203929b1bff5483fe06028a - **Python version**: Python 3.10.8 - **Operating system**: Arch Linux ### What is happening? See title. ### How can we reproduce the issue? ```python import numpy as np from qiskit.circuit import QuantumCircuit from qiskit.extensions.unitary import UnitaryGate from qiskit.primitives import Sampler gate = UnitaryGate(np.eye(2)) circuit = QuantumCircuit(1) circuit.append(gate, [0]) circuit.measure_all() sampler = Sampler() sampler_result = sampler.run([circuit]).result() quasi_dists = sampler_result.quasi_dists ``` ``` Traceback (most recent call last): File "/home/kjs/projects/qiskit-terra/scratch/sampler_hash_bug.py", line 14, in <module> sampler_result = sampler.run([circuit]).result() File "/home/kjs/projects/qiskit-terra/qiskit/primitives/base/base_sampler.py", line 184, in run return self._run( File "/home/kjs/projects/qiskit-terra/qiskit/primitives/sampler.py", line 146, in _run index = self._circuit_ids.get(key) TypeError: unhashable type: 'numpy.ndarray' ``` ### What should happen? It should work. ### Any suggestions? It appears the primitives rely on associating a hashable key with each circuit https://github.com/Qiskit/qiskit-terra/blob/514e38394657802e6cf4aefbf65fe3be3b23b783/qiskit/primitives/utils.py#L127. This is not working. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: [examples] should all examples support the predict stage? This is part of the ongoing effort to sync the example scripts. In https://github.com/huggingface/transformers/issues/10437#issuecomment-789090858 it was flagged that some scripts have test/predict, whereas others don't. Should we: A. have all scripts have train/eval/predict B. only have predict where it's desired @sgugger, @patil-suraj, @LysandreJik Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Move Galata to the `jupyterlab` repo? Opening a new issue since this was originally brought by @fcollonval during the weekly meeting yesterday: https://github.com/jupyterlab/team-compass/issues/117#issuecomment-867008413 Should we move Galata to the `jupyterlab` repository here? Galata currently lives in its own repo under the `jupyterlab` organization: https://github.com/jupyterlab/galata This would make it easier to iterate on it when core PRs make significant changes to the UI for example. For reference there is already the `testutils` package being developed in core lab, that other third-party extensions can depend on for unit tests: https://github.com/jupyterlab/jupyterlab/tree/master/testutils Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: IterableDataset breaks 1.1 compatibility A recently introduced feature unfortunately breaks compability with Pytorch 1.1.0. **Describe the bug** IterableDataset support, introduced in [issue 323](https://github.com/williamFalcon/pytorch-lightning/issues/323), requires Pytorch 1.2.0+. **To Reproduce** In a python environment with Pytorch 1.1.0 do: import pytorch_lightning **Expected behavior** Compatibility with Pytorch 1.1.0. I'm filing it as a bug report rather than a docs fix since the dependency on 1.2.0+ introduced by [issue 323](https://github.com/williamFalcon/pytorch-lightning/issues/323) doesn't seem to be intentional. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: npm@5 breaks linking to extensions As [discussed on gitter](https://gitter.im/jupyterlab/jupyterlab?at=593fd880d83c50560c03ac5f), npm@5 breaks using `jupyter labextension link path/to/extension` because of the changed semantics when handling paths as package specifiers. Here's the npm pull request implementing these changes: https://github.com/npm/npm/pull/15900 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: QuantumCircuit mirror method failure <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: 0.10.0 - **Python version**: 3.6.8 - **Operating system**: MacOS, Ubuntu ### What is the current behavior? The mirror method calls the append method in the circuit passing a tuple while the signature should is: 'append(self, instruction, qargs=None, cargs=None)' causing the append method to fail. This causes Aqua unit test to fail. ### Steps to reproduce the problem ### What is the expected behavior? ### Suggested solutions The problem is at line 191 of quantumcircuit.py. I believe it should be: reverse_circ.append(inst.mirror(), qargs, cargs) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Add flow run information to Slack notification The built-in [Slack notifier](https://docs.prefect.io/core/advanced_tutorials/slack-notifications.html#slack-notifications) is neat but doesn't convey quite enough information to be useful, especially in a "production" context where many users might be running flows simultaneously. Including information about the specific flow *run* (for example, the run name or a link to the flow run in the Cloud UI) would go a long way towards making the notification more informative+actionable. It might also be nice to be able to pass some sort of formatter function to `slack_notifier` that could customize the message at run-time based on information about the task/flow, some variables in the context, things like that. cc @cicdw who it sounds like thinks this would be pretty easy 😁 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: QuantumInstance.execute returns the calibration circuits results <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: 0.18.3 - **Python version**: 3.8.6 - **Operating system**: MacOSX 10.15.7 ### What is the current behavior? When QuantumInstance class uses measurement error mitigation, the `execute` command returns the results of the calibration circuits in addition to the requested circuits. This causes an error in the CircuitSample.sample_circuits command and as a result alters the first iteration of the VQE optimization. ### Steps to reproduce the problem ``` from qiskit import Aer, QuantumCircuit from qiskit.ignis.mitigation import CompleteMeasFitter from qiskit.opflow import CircuitSampler, CircuitStateFn from qiskit.utils import QuantumInstance qc = QuantumCircuit(1) qc.x(0) qc_meas = qc.copy() qc_meas.measure_all() backend = Aer.get_backend('aer_simulator') for idx, is_use_mitigation in enumerate([False, True]): if is_use_mitigation: quantum_instance = QuantumInstance(backend, measurement_error_mitigation_cls=CompleteMeasFitter) else: quantum_instance = QuantumInstance(backend) counts = quantum_instance.execute(qc_meas).get_counts() print(counts) circuit_sampler = CircuitSampler(quantum_instance) sampling = circuit_sampler.sample_circuits(circuit_sfns=[CircuitStateFn(qc)]) print(sampling) ``` ### What is the expected behavior? Should return just the result of the input circuit. ### Suggested solutions It seems like there is a mechanism to skip result in line 641 in utils/quantum_instance.py file. I think it can be utilised to skip the calibration results as well. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Parameters needs examples in the documentation ### What is the expected enhancement? Many users land in https://qiskit.org/documentation/stubs/qiskit.circuit.Parameter.html when search on how to parametrize circuits. @Cryoris did a good jobs at explaining them in https://quantumcomputing.stackexchange.com/questions/13558/how-to-add-several-parameters-in-qiskit-circuit . I think the Parameter docstring needs a short example. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Remove version_checker from client The checks of the remote versions against client versions are no longer done. So we can remove that extra complexity wrapping the requester in the client. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: Forward-mode differentiation rule for 'custom_lin' not implemented Running this code produces the above error. ``` @partial(jax.custom_vjp, nondiff_argnums=(0, 1)) def _clip_gradient(lo, hi, x): return x # identity function def clip_gradient_fwd(lo, hi, x): # return x, None return x, (hi, ) def clip_gradient_bwd(lo, hi, _, g): return (np.clip(g, lo, hi),) _clip_gradient.defvjp(clip_gradient_fwd, clip_gradient_bwd) def clip_gradient(x): lo = -1 hi = x + 1 # causes things to break return _clip_gradient(lo, hi, x) print(jax.grad(clip_gradient)(1.)) ``` Replacing the residual with `None` (see commented out line in `clip_gradient_fwd`) makes the output ``` Traced<ConcreteArray(1.0)>with<JVPTrace(level=1/0)> with primal = DeviceArray(1., dtype=float32) tangent = Traced<ShapedArray(float32[]):JaxprTrace(level=0/0)> ``` I was also able to get a mismatched tracer levels error on a more complex example. To my understanding setting `hi = x + 1` is the issue as it creates a trace of `hi` with `x`. This example may seem a bit contrived, but I originally came across this trying to set an initial step size for `odeint` (see #2604). IIUC we want to make concrete all `JVPTracer` instances that are in static args [here](https://github.com/google/jax/blob/master/jax/custom_derivatives.py#L441). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: Add resuming from specific checkpoint **Is your feature request related to a problem? Please describe.** In current version, there is no way to resume training from a specific checkpoint (not the last checkpoint). Sometimes (very often in my case), one needs experiment training with different hyperparameters (e.g. dropout rate, augmentation) from a specific checkpoint. **Describe the solution you'd like** Add `resume_from_checkpoint`argument to Trainer class. **Describe alternatives you've considered** I tried to use `restore` from Trainer class, but was not successful because it is meant to be used only when .fit() is called. **Additional context** FYI, I made a PR to demonstrate my idea: https://github.com/williamFalcon/pytorch-lightning/pull/516 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Missing f-string in qasm3 export error ### Environment - **Qiskit Terra version**: latest - **Python version**: - **Operating system**: ### What is happening? There is a missing f-string in the following error (L468): https://github.com/Qiskit/qiskit-terra/blob/531e62f3a3c218fee6db116f54ed41ce4e88d9a9/qiskit/qasm3/exporter.py#L466-L469 ### How can we reproduce the issue? Export a circuit with a parametric subroutine. ### What should happen? The name `instruction` should be printed. ### Any suggestions? _No response_ Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: conda=4.1 no longer respects HTTP_PROXY My proxy variables are properly set: ``` $ set https_proxy HTTPS_PROXY=http://myproxy:8080 ``` `conda=4.0.8` successfully picks up my `%HTTPS_PROXY%` and installs `conda=4.1`: ``` $ conda install conda=4.1 Fetching package metadata: .......... Solving package specifications: ......... The following packages will be UPDATED: conda: 4.0.8-py27_0 defaults --> 4.1.0-py27_0 defaults ``` now trying to revert back to `conda=4.0`: ``` $ conda install conda=4.0 Fetching package metadata ......... Could not connect to https://repo.continuum.io/pkgs/free/win-64/ Connection error: HTTPSConnectionPool(host='repo.continuum.io', port=443): Max retries exceeded with url... ``` proxy settings no longer work. Configuring `proxy_servers` in `.condarc` restores connectivity. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the dagster-io/dagster codebase. Here's the problem: dagster-airbyte misidentifies destinations which can support normalization ### Dagster version version 1.2.6 ### What's the issue? https://github.com/airbytehq/airbyte/pull/21005 I believe due to the change above in the Airbyte API (which, as far as I can tell is not reflected in the openapi spec) the dagster-airbyte library can no longer correctly configure a connection to `normalize_data=True`. Last I understood, the dagster Ingestion as Code sources/destinations were code-genned from Airbyte documentation, so it seems the two may have gotten out of sync. ### What did you expect to happen? When I set the connection parameter `normalize_data = True` on a destination that supports normalization, such as Snowflake, I do not receive the exception: `Exception: Destination $destination_name does not support normalization` and my connection configuration is a success. ### How to reproduce? Use Airbyte version `0.43.1` and try to configure a connection with `normalize_data = True` in dagster-airbyte Ingestion as Code. ### Deployment type Dagster Cloud ### Deployment details Right now I'm running this command locally to test, before it hits our CICD. ### Additional information There's an open thread in #airbyte-help in the Airbyte Slack about the openapi spec being out of sync, ~2 weeks old. I've asked for an update on that status, and I'll update here when I receive a response ### Message from the maintainers Impacted by this issue? Give it a 👍! We factor engagement into prioritization. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: compiler object compiles() does not track changes to the files being compiled The compiler object compiles() method does not take into account changes to the file object being compiled. For example, ``` project('foo', 'c') cc = meson.get_compiler('c') test = cc.compiles(files('foo.c')) ``` won't get re-evaluated if `foo.c` changes. I presume the same applies to link() too, but did not try. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Manual for TGate is missing ## Did you find a doc bug or broken link that needs to be fixed? - What is the file name(s) where you found the bug? https://qiskit.org/documentation/apidoc/circuit_library.html#standard-gates - What is the current text that needs to be fixed or removed? (You can copy and paste) There is no page for TGate, while SGate and TdgGate are available. - What should the documentation say instead? TGate should be included in the page. - Are there other related issues or pull requests about this bug? No. ## Does existing documentation need to be updated with new content? - Which files need to be updated? https://qiskit.org/documentation/apidoc/circuit_library.html#standard-gates - What content needs to be updated or replaced? (You can copy and paste) - What new content needs to be added? Page for TGate. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: Conan crash if .count-files consist NULL-character conan version 1.8.0, Windows 7 x64 For some reason (maybe a crash), the .count-files in each conan package in the cache were corrupted and contained a unicode NULL character (https://www.fileformat.info/info/unicode/char/0000/index.htm). This led to a conan crash for basically every package action (e.g. conan info). I already prepared a fix (https://github.com/conan-io/conan/compare/develop...pianoslum:develop) which also adds a little bit more verbosity in case there is no number in the .count-file. Is this enough info or should I elaborate? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: make_exception fails when json.loads fails See [report](https://github.com/GoogleCloudPlatform/gcloud-python/issues/616#issuecomment-74173944) from @pdknsk Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: testing: timeout behavior when testing via `meson test mytestcase` on meson 0.42.0, I am seeing 2 issues: * stdout does not appear to be included in `build/meson-logs/testlog.txt` if the test times out. If it passes or fails, it is included as expected, and stderr is included in all cases. * I haven't found a convenient way to kill the test executable when running the meson test harness. ctrl-C kills the `meson test` parent process, but does not appear to kill the test executable. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: Add `isfinite` support for `datetime64` and `timedelta64` `numpy.isfinite` should support `datetime64` and `timedelta64` objects. It should return `True` for any ordinary value, and `False` for `datetime64('NaT')` and `timedelta64('NaT')`. As a side-effect, this will make `isclose` and `allclose` usable for `datetime64` and `timedelta64` objects. ``` In [97]: numpy.isfinite(numpy.datetime64(10**9, 's')) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-97-8555b18406e5> in <module>() ----> 1 numpy.isfinite(numpy.datetime64(10**9, 's')) TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe'' ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: PubSub: Release the first GA version If no major issues are discovered during the ongoing bake-in period, the PubSub client should be released as GA. Releasing a new version is done with the help of [releasetool](https://github.com/googleapis/releasetool). Prior to the GA release, the following must be done: - Go through the checklist from the internal GA release doc, make sure everything is in order. - Changes in the client lib files: - Update PubSub Python lib README to indicate semver just like Java library has - Update beta tag in PubSub Python lib README - Update beta tag in Python libs root - Set the release level to `ga` in `.repo-metadata.json` - Change beta label in code samples in clients page in Google Cloud website - Add to release notes (talk to @kir-titievsky) - Update any documentation on Cloudsite Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: Add PrefixData, SubdirData, and PackageCacheData to conda/api.py https://github.com/conda/conda/commit/69f1b7af939adb783ee284fa952174e8fa447569#diff-aa516f421733d7851d878e08d4bf7464R408 This is used in conda-build at https://github.com/conda/conda-build/blob/master/conda_build/render.py#L210 Please provide an interface (ideally in conda's exports) that I can use to ask Conda to download packages for me. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the gitpython-developers/GitPython codebase. Here's the problem: CVE-2022-24439: `<gitpython::clone> 'ext::sh -c touch% /tmp/pwned'` for remote code execution This appeared in the CVE feed today: https://security.snyk.io/vuln/SNYK-PYTHON-GITPYTHON-3113858 Not sure if this was reported to you before or not, reporting it here just in case. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: conda-canary ignores CONDA_FORCE_32BIT environment variable Repro: ``` set CONDA_FORCE_32BIT=1 conda create -n test-win32 python=3.5 pywin32 ``` The above command will install a 64bit Python and pywin32 despite `CONDA_FORCE_32BIT` being set to 1. Curiously I can install a 32bit python on its own, but if I then try to install `pywin32` into the same environment it installs the 64bit version which fails (`import win32ui`) with a DLL no a valid win32 application error. **_Aside:**_ It would be nice if the architecture info was shown in the install phase so you would know beforehand that it was attempting to install the wrong architecture version Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: extreme truncating of return values while stepping through a function, when printing return values, ipython truncates them quite a bit - you get things like ``` <Context...ble.txt'> ``` Where in the code is this done? I haven't been able to find it. I want to give it more room - at least 80 chars wide would be fine. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Add date attribute to BasicAer job result ### What is the expected enhancement? This is a practical improvement because it aligns the API with AerJob. It is also required according to https://arxiv.org/abs/1809.03452. See https://github.com/Qiskit-Partners/mthree/issues/94 for context. add date to all Result objects - QAMP <!-- ⚠ If you do not respect this template, your pull request will be closed. ⚠ Your pull request title should be short detailed and understandable for all. ⚠ Also, please add a release note file using reno if the change needs to be documented in the release notes. ⚠ If your pull request fixes an open issue, please link to the issue. - [ ] I have added the tests to cover my changes. - [ ] I have updated the documentation accordingly. - [ ] I have read the CONTRIBUTING document. --> ### Summary Executing the following code gives an error because BasicAer backend job has no attribute date. Fixes #7781 ``` python import numpy as np import mthree from qiskit import BasicAer, QuantumCircuit, Aer backend = BasicAer.get_backend("statevector_simulator") mit = mthree.M3Mitigation(backend) mit.cals_from_system(range(2)) circuit = QuantumCircuit(2) circuit.rx(np.pi / 4, 0) circuit.rx(np.pi / 2, 1) circuit.measure_all() ``` ### Details and comments This error can be solved by putting the attribute`job.result().date = None` as a default parameter. Part of https://github.com/qiskit-advocate/qamp-spring-22/issues/37 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Bug: Finetuning large models resume checkpoint error When finetuning a large model (e.g. Eleuther 6B), you shard the checkpoints upon saving [here](https://github.com/huggingface/transformers/blob/c79bbc3ba54a81dab2eac13d89f264ed64cb2460/src/transformers/modeling_utils.py#L193). However, upon resuming the checkpoint (and loading the best checkpoint after training), you confirm if there is a valid checkpoint assuming weights are no sharded [here](https://github.com/huggingface/transformers/blob/dced262409177586bb510b6b724c762fb89da0e8/src/transformers/trainer.py#L1196). This causes an error upon resuming training. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Compatibility classes for converting BackendV1 to BackendV2 to facilitate migration ### What should we add? For package developers trying to transition to new backends it would be very convenient if terra had wrapper backend classes/functions that can make a backend V1 into a backend V2 and vice versa. Something to this effect was [recently added to qiskit-experiments](https://github.com/Qiskit/qiskit-experiments/blob/main/qiskit_experiments/framework/backend_data.py#L23) to help facilitate handling both types of backends in tests, however it falls a bit short of general use because it uses duck-typing of methods for both backends but wont actually be an instance of a backend so can't be used as a drop-in replacement. It would be convenient having either a backend class or generator function that can take one backend and return an equivalent instance of the other. Eg we could have classes that can be initialized with another backend like: ```python class WrappedBackendV1(BackendV1): def __init__(self, backend: Union[BackendV1, BackendV2]): class WrappedBackendV2(BackendV2): def __init__(self, backend: Union[BackendV1, BackendV2]): ``` An alternative would be a function to generate a backend either V1->V2 or V2->V1 (or trivially V1->V1, V2->V2) ```python # function interface def wrapped_backend( backend: Union[BackendV1, BackendV2], target_cls=BackendV2 ) -> Union[BackendV1, BackendV2] ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: Issue with f2py in Numpy 1.13 when character arrays appear in a callback function There is an issue with f2py in Numpy 1.13 when character arrays appear in a callback function. The following example works with Numpy 1.12 but not in 1.13: ``` #! /usr/bin/env python from __future__ import print_function import numpy from subprocess import call # # build extension from FORTRAN source # source = """ subroutine func_with_callback(callBack, cu, lencu) implicit none integer :: lencu character*8 cu(lencu) external callBack print *,'Lencu:', lencu print *,'Calling callback...' call callBack(cu, lencu) print *,'Back in fortran...' end subroutine func_with_callback """ with open("callback.f", "w") as src_file: src_file.write(source) rc = call("f2py callback.f -m callback -h callback.pyf".split()) if rc: quit() rc = call("f2py -c callback.pyf callback.f".split()) if rc: quit() # # define callback function # def callBack(cu, lencu): print ('In callback:', cu) # # call library function with callback # from callback import func_with_callback print(func_with_callback.__doc__) print("\nNumpy Version:", numpy.__version__, "\n") cu = numpy.zeros((1, 8), 'c') func_with_callback(callBack, cu) ``` ================ Numpy Version: 1.12.1 Lencu: 1 Calling callback... In callback: [['' '' '' '' '' '' '' '']] Back in fortran... ================ Numpy Version: 1.13.3 Lencu: 1 Calling callback... Call-back cb_callback_in_func_with_callback__user__routines failed. Traceback (most recent call last): File "test_callback.py", line 57, in <module> func_with_callback(callBack, cu) ValueError: data type must provide an itemsize Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: PIN 16: Add `CustomResult` that will be used to hydrate user Results from cloud states ## Use Case See [PIN 16](https://docs.prefect.io/core/PINs/PIN-16-Results-and-Targets.html) for more motivation on new style Result classes. Today, users may provide their own custom `ResultHandler` subclasses that do not serialize to Cloud; we expect to support the same for custom new style `Result` subclasses. ## Solution Add a `CustomResult` that wraps any custom result handler implementation or Result subclass from the user that we can serialize to Cloud and instantiate in `State._result` for a user when hydrating States from Cloud. The important method to implement is: `CustomResult.hydrate(result: Result) -> Result` This should return an instance of the result arg, since the pipeline will call this a la `state._result.hydrate(result=self.task.result)`. Other methods common to Results like store_safe_value, validate, read, write etc should not be implemented. (Decide if it should raise its own kind of warning or not especially if we miss an edge case and then get the NotImplementedError from tbhe base class.) ## Alternatives *Please describe any alternatives you've considered, even if you've dismissed them* Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: Save checkpoint for the last epoch How to save the checkpoint only for the last epoch? In the docs: ``` if save_top_k == k, the best k models according to the quantity monitored will be saved. if save_top_k == 0, no models are saved. if save_top_k == -1, all models are saved. Please note that the monitors are checked every period epochs. if save_top_k >= 2 and the callback is called multiple times inside an epoch, the name of the saved file will be appended with a version count starting with v0. ``` * `k = 0` does not save any. * `k > 1` saves only a few the best * `k = -1` saves all of them Currently, I am using k = -1, but it space consuming. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: conda xontrib xonsh wrapper Make a wrapper for xonsh. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Allow users to choose transaction isolation level? I believe we currently only support the default transaction isolation level for Datastore (`snapshot`). Could we figure out a way to allow people to choose a `serializable` transaction? See https://cloud.google.com/datastore/docs/apis/v1beta2/datasets/beginTransaction Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: PerceiverAudioPreprocessor: forward() missing 1 required positional argument: 'pos' The [`forward()` method implementation of `PerceiverAudioPreprocessor`](https://github.com/huggingface/transformers/blob/38cc35069c10d153e872162265288263bb7394b7/src/transformers/models/perceiver/modeling_perceiver.py#L3267) seems to be problematic because it has an extra required `pos` argument, whereas all other preprocessors do not (or it is optional). In fact, while it is passed to `_build_network_inputs()`, `pos` is not actually used in that method. Hence, I am not sure why it exists. Moreover, it breaks the default `PerceiverModel` operation, because that class assumes that there only one positional argument called `inputs` [when calling the preprocessor](https://github.com/huggingface/transformers/blob/38cc35069c10d153e872162265288263bb7394b7/src/transformers/models/perceiver/modeling_perceiver.py#L865). This seems to be a serious issue in my opinion because it crashes any instantiation of `PerceiverModel` with a `PerceiverAudioPreprocessor` as `input_preprocessor`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the celery/celery codebase. Here's the problem: Replaced task does not complete when replacement sig is a group (4.0.2) ## Checklist - [x] I have included the output of ``celery -A proj report`` in the issue. ``` software -> celery:4.0.2 (latentcall) kombu:4.0.2 py:2.7.11 billiard:3.5.0.2 py-amqp:2.1.4 platform -> system:Darwin arch:64bit imp:CPython loader -> celery.loaders.app.AppLoader settings -> transport:amqp results:redis://localhost:6379/0 broker_url: u'amqp://guest:********@localhost:5672//' result_backend: u'redis://localhost:6379/0' ``` (The above output is against `master`.) Also: ``` (foo) $ pip freeze | grep redis redis==2.10.5 ``` - [x] I have verified that the issue exists against the `master` branch of Celery. ## Steps to reproduce *foo.py:* ```python from celery import Celery, group app = Celery('foo', broker='amqp://guest:guest@localhost:5672//', backend='redis://localhost:6379/0') @app.task def multiply(a, b): return a * b @app.task(bind=True) def multiply_by_two(self, num): raise self.replace(multiply.s(num, 2)) @app.task(bind=True) def multiply_all_by_two(self, nums): subtasks = [multiply_by_two.s(n) for n in nums] raise self.replace(group(*subtasks)) ``` *bar.py:* ```python from foo import multiply_by_two, multiply_all_by_two if __name__ == '__main__': print multiply_by_two.delay(3).get() # completes in 4.0.1 and 4.0.2 print multiply_all_by_two.delay([1, 2, 3]).get() # completes in 4.0.1; does not complete in 4.0.2 ``` ## Expected behavior A replaced task should complete when the replacement sig is a group (and does in 4.0.1). ## Actual behavior A replaced task does not complete when the replacement sig is a group (in 4.0.2). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: Docstring for jax.lax.tie_in `jax.lax.tie_in` seems to have subtle but important properties, but [has no docstring](https://jax.readthedocs.io/en/latest/_autosummary/jax.lax.tie_in.html#jax.lax.tie_in). Could we add one? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Rewrite Variational Quantum Deflation with primitives. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Support for DMD -makedeps switch A new feature has recently been merged into DMD (see dlang/dmd#12011) to implement emission of dependency file in Makefile format. This should be available in DMD v2.096, and in LDC when it will use the DMD frontend of the same version. Meson can add this switch to the ninja D language rules in order to have correct dependencies and retrigger builds in an appropriate way. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: docker-compose config --volumes In addition to ``` $ docker-compose config --services ``` it'd be nice to have ``` $ docker-compose config --volumes ``` listing the named volumes similarly to services. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Notebook docs touchup Cleaning up outstanding issues in notebook.rst. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: Possible issue with partial gradient application I'm trying to define the derivative of a function at a point, for then compiling it with jit, but either I'm not doing it in the right way (with functools.partial) or there is a problem somewhere. Define a simple function of x and y and its derivative with respect to x: ```python from jax import grad def f(x,y): return x+y df = grad(f, argnums=0) ``` This works: ```python from functools import partial partial(f, x = 0.)(y = 1) # 1.0 ``` This doesn't: ```python from functools import partial partial(df, x = 0.)(y = 1) # IndexError: tuple index out of range ``` why? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: --backend=vs2019 DebugInformationFormat is not set correctly **Describe the bug** DebugInformationFormat is set in the Configuration PropertyGroup, but Visual Studio 2019 only reads it from the ClCompile section. It looks like vs2010backend.py accidentally sets DebugInformationFormat=EditAndContinue in type_config instead of clconf. (Possibly BasicRuntimeChecks too). It's possible that older Visual Studio wants this value outside ClCompile. I didn't check, but it seems unlikely. **To Reproduce** meson --backend=vs2019 --buildtype=debug <any source dir> **Expected behavior** Projects built with the default debug configuration in visual studio (not from ninja) should be built with /ZI (Program Database for Edit and Continue). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: run -d message unclear Prior to 1.0.dev, (0.12.1), I had to hit 'c' to start the script: ``` IPython 0.12.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. In [1]: run -d foo.py ERROR: File `u'foo.py'` not found. In [2]: pwd Out[2]: u'/Users/mhearne/src/python/scipy2013/ipython/ipython-in-depth/notebooks/figs' In [3]: cd /Users/mhearne/src/python /Users/mhearne/src/python In [4]: run -d foo. foo.py foo.pyc In [4]: run -d foo.py *** Blank or comment *** Blank or comment Breakpoint 1 at /Users/mhearne/src/python/foo.py:3 NOTE: Enter 'c' at the ipdb> prompt to start your script. > <string>(1)<module>() ipdb> c > /Users/mhearne/src/python/foo.py(3)<module>() 2 1---> 3 x = 1 4 print 'hello world' ``` With 1.0.dev, it behaves like this ('c' not required): ``` In [1]: !cat foo.py #!/usr/bin/env python x = 1 print 'hello world' In [2]: run -d foo foo.py foo/ foolog.py In [2]: run -d foo.p foo.py foo.pyc In [2]: run -d foo.py *** Blank or comment *** Blank or comment *** Blank or comment NOTE: Enter 'c' at the ipdb> prompt to start your script. > /Users/mhearne/src/python/foo.py(3)<module>() 2 ----> 3 x = 1 4 print 'hello world' ``` If this is the intended behavior, I suggest removing the misleading message. Looks like @tkf implemented this change, @ivanov said to mention him. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Tsconfig references are not being popultated <!-- Welcome! Before creating a new issue: * Search for relevant issues * Follow the issue reporting guidelines: https://jupyterlab.readthedocs.io/en/latest/getting_started/issue.html --> ## Description While working on #8747 we noticed that the `tsconfig` references were not being properly updated for `debugger` and `metapackage` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the dagster-io/dagster codebase. Here's the problem: Create dagster-graphql CLI Should replace dagit -q and used in integrations like airflow Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Trait default values are validated even when not ever used ``` Python from IPython.utils.traitlets import * class Foo(HasTraits): bar = Type(allow_none=False) foo = Foo(bar=int) ``` yields `The 'bar' trait of a Foo instance must be a subclass of object, but a value of type 'NoneType' (i.e. None) was specified.` The default value is validated while it is not needed. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Templating for ShellTask commands Opening for discussion; we could go for a full-fledge solution like Jinja, _or_ we could do something simple like: ``` echo !param ``` and replace all instances of `!string` with a parameter value (either taken from context or from an actual `Parameter`). [The exclamation point should be a safe character to rely on](https://unix.stackexchange.com/questions/3747/understanding-the-exclamation-mark-in-bash). I'm not really sure how heavily people will use templating, and how intricate their use cases will be. **cc:** @jlowin @joshmeek Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Schedule drawing fails if schedule is empty <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information - **Qiskit Terra version**: master - **Python version**: 3.7 - **Operating system**: OsX ### What is the current behavior? Schedule drawing fails if schedule is empty ### Steps to reproduce the problem ```python from qiskit import pulse fc_pi = pulse.FrameChange(np.pi) dc0 = pulse.DriveChannel(0) fc_pi_dc0 = fc_pi.to_instruction(dc0) sched = pulse.Schedule() sched += fc_pi_dc0 sched.draw() ``` ### What is the expected behavior? ### Suggested solutions Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Cannot compile spice when cross compiling **Describe the bug** Worked under 0.56.2. Broke with 0.57 **To Reproduce** https://gitlab.freedesktop.org/spice/spice/-/blob/master/meson.build I guess. **Expected behavior** Compile **system parameters** * cross build * Fedora 33 * Python 3.9.2 * latest master - 0.57.1 tested * 1.10.2 Sample log: https://downloads.openwrt.org/snapshots/faillogs/mips64_octeonplus/packages/spice/compile.txt Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: conda run doesn't respect the documented "--" option ## Current Behavior The documented `--` flag for `conda run` is very useful; lacking it, you can't run programs that share command-line arguments with `conda run`. It doesn't work, though. ### Steps to Reproduce ``` # conda run -n myenv -- echo hello /opt/conda/envs/myenv/.tmp7xhfcesk: line 3: --: command not found ERROR conda.cli.main_run:execute(39): Subprocess for 'conda run ['--', 'echo', 'hello']' comma nd failed. Stderr was: /opt/conda/envs/myenv/.tmp7xhfcesk: line 3: --: command not found ``` ## Expected Behavior I would expect, as per the documentation, that this would run `echo hello` within the environment. ## Environment Information This happens in Conda 4.8.1 as well as earlier versions. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: GPU memory show max/min only Instead of logging GPU mem for all GPUs, probably better to just show the min/max usage? Maybe the flag can be modified? ```python # now Trainer(log_gpu_memory=False) # proposed Trainer(log_gpu_memory='min_max') # and for all GPUs Trainer(log_gpu_memory='all') ``` @adefazio Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the conda/conda codebase. Here's the problem: put ftp:// back into 4.2 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: LayoutLMv3: Pre-training for Document AI with Unified Text and Image Masking ### Model description LayoutLMV3 is the successor of the LayoutLM models. the models are specialized in multimodal document analysis tasks and achieve SOTA results on them. The current [code](https://github.com/microsoft/unilm/blob/master/layoutlmv3/layoutlmft/models/layoutlmv3/modeling_layoutlmv3.py) for the LayoutLMV3 is implemented in huggingface format. Since the code is already more similar to the Huggingface format, I am not sure whether integrating this model into this repo is necessary, but there will be an ease of use if it is available in the library itself. ### Open source status - [X] The model implementation is available - [X] The model weights are available ### Provide useful links for the implementation Model Implementation: https://github.com/microsoft/unilm/tree/master/layoutlmv3 Model Weights: https://huggingface.co/microsoft/layoutlmv3-base Authors: Yupan Huang,Tengchao Lv, Lei Cui, Yutong Lu ,Furu Wei Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: "Both `max_new_tokens` and `max_length` have been set but they serve the same purpose" when only setting max_new_tokens. ### System Info - `transformers` version: 4.27.0.dev0 - Platform: Windows-10-10.0.19044-SP0 - Python version: 3.10.4 - Huggingface_hub version: 0.12.0 - PyTorch version (GPU?): 1.13.1+cpu (False) - Tensorflow version (GPU?): not installed (NA) - Flax version (CPU?/GPU?/TPU?): not installed (NA) - Jax version: not installed - JaxLib version: not installed - Using GPU in script?: No - Using distributed or parallel set-up in script?: No ### Who can help? @gante I believe. ### Information - [ ] The official example scripts - [X] My own modified scripts ### Tasks - [X] An officially supported task in the `examples` folder (such as GLUE/SQuAD, ...) - [ ] My own task or dataset (give details below) ### Reproduction 1. Install transformers 2. Run the following script ``` from transformers import pipeline summarizer = pipeline("summarization", max_new_tokens=50) prompt = "text to summarize" summary = summarizer(prompt) ``` 3. It crashes with the following error: > ValueError: Both `max_new_tokens` and `max_length` have been set but they serve the same purpose -- setting a limit to the generated output length. Remove one of those arguments. Please refer to the documentation for more information. (https://huggingface.co/docs/transformers/main/en/main_classes/text_generation) ### Expected behavior Expected behavior is that the script should run. I only set `max_new_tokens` and not `max_length`. This might seem like a duplicate of https://github.com/huggingface/transformers/issues/20894 but the issue persists even after installing the latest version of transformers with the fix for that issue. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: nditer.__next__ keeps working after `close` is called @mattip. This surprises me a little: ```python >>> it = np.nditer(np.arange(3)) >>> next(it) array(0) >>> it.close() >>> next(it) array(1) >>> next(it) array(2) >>> next(it) StopIteration ``` Compare with ```python >>> def generator(): ... yield from range(3) >>> it = generator() >>> next(it) 0 >>> it.close() >>> next(it) StopIteration ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the docker/compose codebase. Here's the problem: UnicodeEncodeError: 'ascii' codec can't encode character u'\u2023' When trying to install `RUN /bin/bash -l -c 'passenger-install-nginx-module --auto --auto-download --prefix=/opt/nginx'` from Docker, I get: ``` Traceback (most recent call last): File "<string>", line 3, in <module> File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.main", line 39, in main File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 21, in sys_dispatch File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.command", line 31, in dispatch File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 24, in dispatch File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.command", line 50, in perform_command File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.docopt_command", line 27, in perform_command File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.cli.main", line 108, in build File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.project", line 123, in build File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.service", line 313, in build File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.service", line 374, in stream_output File "/Users/nonsense/code/fig/build/fig/out00-PYZ.pyz/fig.service", line 419, in print_output_event UnicodeEncodeError: 'ascii' codec can't encode character u'\u2023' in position 2: ordinal not in range(128) ``` I guess the reason is that at this point nginx shows a list of languages and there is a unicode character used as a bullet point in front of each language. fig version is: 0.4.1 docker version is: Client version: 0.11.1 Client API version: 1.11 Go version (client): go1.2.1 Git commit (client): fb99f99 Server version: 0.11.1 Server API version: 1.11 Git commit (server): fb99f99 Go version (server): go1.2.1 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: `DensityMatrix.partial_transpose` does not preserve input dimensions ### Environment - **Qiskit Terra version**: to be released in 0.24.0 - **Python version**: 3.10 - **Operating system**: MacOS ### What is happening? The `partial_transpose` should return a density matrix of the same dimensionality as the input `DensityMatrix` object. When the dimensions are for systems different than qubits, the dimensions are currently not preserved. ### How can we reproduce the issue? For in the following example, the dimensions of the output density matrix ρ2 are (9,) but they should be (3,3). ```python >>> import numpy as np >>> from qiskit.quantum_info import Statevector, DensityMatrix >>> ψ = Statevector(np.array([1,0,0,0,1,0,0,0,1])*1/np.sqrt(3),dims=(3,3)) >>> ρ1 = DensityMatrix(ψ) >>> ρ1.dims() (3, 3) >>> ρ2 = ρ1.partial_transpose([0]) >>> ρ2.dims() (9,) ``` ### What should happen? It should be an easy fix. The function should return: ```python return DensityMatrix(rho, dims=self.dims()) ``` instead of just: ```python return DensityMatrix(rho) ``` ### Any suggestions? _No response_ Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Please cut new release of Cloud Storage Please cut a release to include https://github.com/GoogleCloudPlatform/google-cloud-python/pull/5877 (Object Lifecycle Management) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: Switch from print to logging Use logging instead of print. (@Ir1d you brought this up before) Suggested by @adefazio Switch from print to logging Use logging instead of print. (@Ir1d you brought this up before) Suggested by @adefazio Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: BigTable Row Data cells property not copy **Is your feature request related to a problem? Please describe.** I was profiling the code I wrote that makes use of the BigTable client python API. I realised that it made a lot of calls to `deepcopy` and that these calls were very costly. It's actually because the `cells` property of a [row data](https://googleapis.github.io/google-cloud-python/latest/bigtable/row-data.html#cells) is actually returning a deep copy of the actual private `_cells` property. The fact is that I don't need all the cells information and I am only using it once so I don't really need the copy. **Describe the solution you'd like** I think it would be nice to have the possibility to return the `_cells` property directly without copying. I imagine there are reasons why it has been coded like that, not offering the alternative, but I don't see them. **Describe alternatives you've considered** Of course a hacky solution is to access directly the private property but it doesn't look like the right way to do it (i.e. `row._cells`). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the google/jax codebase. Here's the problem: Unimplemented: binary integer op 'power' ```python def square(x): return x**2 val = 3 dfn = grad(square) print(dfn(val)) ``` I was surprised this threw an error. Changing it to `val = 3.0` works as expected. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Should we compare Entity._meanings in __eq__ /cc @tseaver @pcostell Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Ensure that libraries are designated alpha. As part of the refresh for `core>=0.23.0` and HTTP headers, please also ensure that all client libraries are designated alpha in `setup.py` _except_ the following, which are beta: * BigQuery * Datastore * Logging * Storage This should be altered as part of the umbrella release (should be trivial). Thank you. :-) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: IPython.utils.columnize sometime wrong... ``` python In [1]: import IPython.utils.text as ut ...: len(ut.columnize(['x'*40,'x'*40],displaywidth=80).split('\n')[0]) Out[1]: 82 # should be < 80 ``` two 40 letters words separated by 2 char could not enter on a 80 char line. should be 2 times 40(+separator size maybe) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Pagination doesn't work with tags filter **Apache Airflow version**: 2.0.1 **Environment**: - **OS**: Linux Mint 19.2 - **Kernel**: 5.5.0-050500-generic #202001262030 SMP Mon Jan 27 01:33:36 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux **What happened**: Seems that pagination doesn't work. I filter DAGs by tags and get too many results to get them at one page. When I click second page I'm redirected to the first one (actually, it doesn't matter if I click second, last or any other - I'm always getting redirected to the first one). **What you expected to happen**: I expect to be redirected to the correct page when I click number on the bottom of the page. **How to reproduce it**: 1. Create a lot of DAGs with the same tag 2. Filter by tag 3. Go to the next page in the pagination bar **Implementation example**: ``` from airflow import DAG from airflow.utils.dates import days_ago for i in range(200): name = 'test_dag_' + str(i) dag = DAG( dag_id=name, schedule_interval=None, start_date=days_ago(2), tags=['example1'], ) globals()[name] = dag ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Option precedence is inconsistent Which of several conflicting options is applied is not consistent. ``` cd "test cases/common/1 trivial" meson build --bindir=foo --bindir=bar -Db_sanitize=address -Db_sanitize=thread meson configure build ``` Expected: `bindir=bar` `b_sanitize=thread` Actual: `bindir=bar` `b_sanitize=address` Affected: At least 0.43.0 to 0.46.0. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: "Modulus" refers to normalizing by largest singular value in docs https://github.com/numpy/numpy/blob/33415905e85c51c3348c1def9dfa306fbd358b5e/numpy/linalg/linalg.py#L1903-L1904 ^ This code from master corresponds to the documentation for [numpy.linalg.pinv](https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.pinv.html?highlight=modulus): > Singular values smaller (in modulus) than _rcond * largest_singular_value_ (again, in modulus) are set to zero. Note that singular values cannot be complex. They are always real and non-negative. And so this is a confusing use of the term "modulus" to me. From what I can see, the singular values are normalized by the largest value. For example, if `s = [2. 1. 0.]` and `rcond = 1e-15`, then `cutoff = 2e-15` and so `s > cutoff` is effectively normalizing `s` by the largest singular value (2) before comparing to `rcond` (i.e., by cross-multiplying). https://github.com/numpy/numpy/blob/33415905e85c51c3348c1def9dfa306fbd358b5e/numpy/linalg/linalg.py#L1968-L1969 Perhaps I misunderstand the usage of this term, but I think it would be more appropriate to say something like...? > Singular values smaller than rcond (normalized such that the largest singular value is one) are set to zero. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software debugging assistant. Help debug issues by analyzing problems systematically and providing clear, step-by-step reasoning.

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: f2py with "associate" <-> "end associate" f2py break with functions/subroutines containing associate construct. my hack ``` diff diff --git a/numpy/f2py/crackfortran.py b/numpy/f2py/crackfortran.py index 5d664e3..009fa3e 100755 --- a/numpy/f2py/crackfortran.py +++ b/numpy/f2py/crackfortran.py @@ -470,7 +470,7 @@ beginpattern90=re.compile(beforethisafter%('',groupbegins90,groupbegins90,'.*'), groupends=r'end|endprogram|endblockdata|endmodule|endpythonmodule|endinterface' endpattern=re.compile(beforethisafter%('',groupends,groupends,'[\w\s]*'),re.I),'end' #endifs='end\s*(if|do|where|select|while|forall)' -endifs='(end\s*(if|do|where|select|while|forall))|(module\s*procedure)' +endifs='(end\s*(if|do|where|select|while|forall|associate))|(module\s*procedure)' endifpattern=re.compile(beforethisafter%('[\w]*?',endifs,endifs,'[\w\s]*'),re.I),'endif' # implicitpattern=re.compile(beforethisafter%('','implicit','implicit','.*'),re.I),'implicit' ``` Can you help me debug this systematically and explain your reasoning?