[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: Added retry on internal error Added retry on internal error as suggested by the internal error message: '500 Error encountered during execution. Retrying may solve the problem.'. Rationalised the conditions structure so it would simplify addition of other retry conditions. 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 JohnSnowLabs/spark-nlp codebase. Here's the problem: DocumentAssembler on array<string> ### Is there an existing issue for this? - [X] I have searched the existing issues and did not find a match. ### Who can help? _No response_ ### What are you working on? I don't know why but my question was deleted. Therefore, I will repeat again. I am working with a dataframe that I need to lemmatize. There, the input is an array of strings. I am trying to use DocumentAssembler for array of strings. The documentation says: "The DocumentAssembler can read either a String column or an Array[String])". But it doesn't work like that for me. Can you explain what I'm doing wrong? Or is the documentation out of date? ### Current Behavior I am getting an error ``` AnalysisException: [CANNOT_UP_CAST_DATATYPE] Cannot up cast input from "ARRAY<STRING>" to "STRING". The type path of the target object is: - root class: "java.lang.String" You can either add an explicit cast to the input data or choose a higher precision type of the field in the target object ``` ### Expected Behavior - ### Steps To Reproduce When I do a simple example: ``` data = spark.createDataFrame([[["Spark NLP is an open-source text processing library."]]]).toDF("text") documentAssembler = DocumentAssembler().setInputCol("text").setOutputCol("document") result = documentAssembler.transform(data) result.select("document").show(truncate=False ``` ### Spark NLP version and Apache Spark sparknlp.version() == '4.4.0' spark.version == '3.4.0' ### Type of Spark Application _No response_ ### Java Version _No response_ ### Java Home Directory _No response_ ### Setup and installation _No response_ ### Operating System and Version _No response_ ### Link to your project (if available) _No response_ ### Additional Information _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 huggingface/transformers codebase. Here's the problem: Pipeline “zero-shot-classification” gives “TypeError: __call__() takes 2 positional arguments but 3 were given.” - `transformers` version: 4.11.0.dev0 - Platform: Linux-4.9.253-rt168-tegra-aarch64-with-debian-buster-sid - Python version: 3.6.13 - PyTorch version (GPU?): 1.9.0 (True) - 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?: (True) - Using distributed or parallel set-up in script?: (False) @LysandreJik ## Information Model I am using (‘facebook/bart-large-mnli’): The problem arises when using: the official example scripts: (basically) ```python from transformers import pipeline classify=pipeline('zero-shot-classification') text=("Give me a weather report") tags=["request_weather", "catch_fire"] classify(text, tags) ``` The tasks I am working on is: my own task or dataset: It’s a bunch of ugly hacks on each other’s shoulders, in a trench coat, masquerading as a Python script. ## To reproduce Steps to reproduce the behavior: 1. Run script Result: ```bash Traceback (most recent call last): File "test.py", line 8, in <module> classify(text, tags) TypeError: __call__() takes 2 positional arguments but 3 were given ``` ## Expected behavior Literally anything but this. I am very confused. Please help, very much appreciated, getting gray hairs from this, thanks! 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: Unnecessary warnings during airflow pods starts ### Apache Airflow version 2.2.2 (latest released) ### What happened Warnings `{providers_manager.py:156} WARNING - Exception when importing 'airflow.providers.google.leveldb.hooks.leveldb.LevelDBHook' from 'apache-airflow-providers-google' package: No module named 'plyvel'` appear in `wait-for-airflow-migrations` init containers and during webserver pod start. ### What you expected to happen No such warnings, they were not present in 2.1.3 version. ### How to reproduce Install Airflow using airflow helm chart with 2.2.2 airflow docker image and check `wait-for-airflow-migrations` init containers logs. Warnings can also be seen in webserver container. ### Operating System Debian “buster” ### Versions of Apache Airflow Providers Providers that come with the official Airflow docker image. ### Deployment Official Apache Airflow Helm Chart ### Deployment details _No response_ ### Anything else Looking at commit history, isn't this supposed to be a debug level log as per https://github.com/apache/airflow/commit/2f32df7b711cf63d18efd5e0023b22a79040cc86#diff-c56df299b30e60d690494057a4e8721d36406c0cca266961ff2ae6504993c8cb ? Seems like this logic was changed in https://github.com/apache/airflow/commit/29aab6434ffe0fb8c83b6fd6c9e44310966d496a#diff-c56df299b30e60d690494057a4e8721d36406c0cca266961ff2ae6504993c8cbL288 since `_sanity_check` doesn't handle `ImportError`s as debug messages . Should these warnings be ignored for now? ### Are you willing to submit 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 PrefectHQ/prefect codebase. Here's the problem: Warning on `ifelse`/`merge` use ## Description I can't seem to find any combination of `ifelse`/`merge` usage that doesn't give me the `UserWarning: Tasks were created but not added to the flow` warning. ## Expected Behavior No warning ## Reproduction ```python from prefect import Flow, task from prefect.tasks.control_flow.conditional import ifelse, merge @task def a(x): return x + 1 @task def b(x): return x * 2 with Flow('f') as flow: x = 2 t1 = a(x) t2 = b(x) ifelse(x > 1, t1, t2) y = merge(t1, t2) flow.run() # UserWarning: Tasks were created but not added to the flow ``` Is there something going on in the example above I may be misunderstanding? 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: Put parameters into context inside of a flow run When a flow runner is in a cloud context it makes a call to the client's `get_flow_run_info` function. That call queries for the parameters, version, and current_state. The parameters however are not used. Inside the flow runner it can take those parameters (from its `flow_run_info` object that it creates) and set it in the context here -> https://github.com/PrefectHQ/prefect/blob/master/src/prefect/engine/flow_runner.py#L189 if there are no other parameters passed into the runner. 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: deepsource.io issue analysis Maybe useful to start improving the codebase. https://deepsource.io/gh/jaipradeesh/GitPython/issues/ 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: Option to disable printing logstate on log activation /usr/lib/python2.7/site-packages/IPython/core/magics/logging.py Line 135 printing the log state everytime shell is opened is annoying, please make it configurable. 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 hooks exceptions show not useful stack trace Having a hook raising an ``Exception`` produces something like: ```bash ERROR: [HOOK - name_conventions.py] pre_export(): Reference Hello/0.1@user/testing should be all lowercase Traceback (most recent call last): File "c:\users\memsharded\envs\conanpip\lib\site-packages\conans\client\hook_manager.py", line 56, in execute method(output=output, **kwargs) File "C:\Users\memsharded\.conan\hooks\name_conventions.py", line 4, in pre_export raise Exception("Reference %s should be all lowercase" % ref) Exception: Reference Hello/0.1@user/testing should be all lowercase ``` As this is not very useful, I suggest removing it. 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: Serialize State in New Triggers With #947 merged, we now have triggers (and have always had `cache_validators`) which carry _state_. However, when we serialize them to Cloud, we only carry their names for display in the UI. It would be a very nice-to-have if we could serialize the state as well, i.e., serialize the bounds in the triggers and the validation lists in the curried cache validators for display in the UI. 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: display.FileLinks should work in the exported html verion of a notebook It would be nice to have the output of FileLinks work in the exported html version of a notebook. Would this be as simple as using relative file-paths? 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: Support mapping specific ports in "docker-compose run" It should be possible to pass the `-p` option to expose ports when doing `docker-compose run`. It should probably be not be possible to use this option in combination with the `--service-ports` option. This is part of #363. 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: function to calculate 2-qubit gate depth <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues to confirm this idea does not exist. --> ### What is the expected behavior? Currently `circuit.depth()` considers all gates in the circuit. In the context of present experiments 2-qubit gates are often much longer than 1-qubit gates, so a function `circuit.depth_2q_gates()` would be useful. This would be a better estimate of true depth cost. Of course the most accurate would be to schedule the circuit with the gate durations and look at `circuit.duration`, but that requires further compilation and is not a pure analysis of the circuit. 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: docs Snippet only includes half of documentation Small problem with `snippets_table.py` for `google.cloud.bigtable.row.DirectRow.clear` [documentation](https://googleapis.github.io/google-cloud-python/latest/bigtable/row.html#google.cloud.bigtable.row.DirectRow.clear) only showing half the example code (e.g. not actually showing the running of the clear command) ![Screenshot from 2019-03-16 10-42-40](https://user-images.githubusercontent.com/10172976/54479283-77cde100-47d8-11e9-85e1-9441878653a4.png) This is because the test has two parts and the snippit is only including the first. ``` def test_bigtable_row_clear(): # [START bigtable_row_clear] from google.cloud.bigtable import Client client = Client(admin=True) instance = client.instance(INSTANCE_ID) table = instance.table(TABLE_ID) row_key = b"row_key_1" row_obj = table.row(row_key) row_obj.set_cell(COLUMN_FAMILY_ID, COL_NAME1, b"cell-val") # [END bigtable_row_clear] mutation_size = row_obj.get_mutations_size() assert mutation_size > 0 # [START bigtable_row_clear] row_obj.clear() # [END bigtable_row_clear] mutation_size = row_obj.get_mutations_size() assert mutation_size == 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 apache/airflow codebase. Here's the problem: Handle TODO: .first() is not None can be changed to .scalar() ### Body The TODO part of: https://github.com/apache/airflow/blob/d67ac5932dabbf06ae733fc57b48491a8029b8c2/airflow/models/serialized_dag.py#L156-L158 can now be addressed since we are on sqlalchemy 1.4+ and https://github.com/sqlalchemy/sqlalchemy/issues/5481 is resolved ### Committer - [X] I acknowledge that I am a maintainer/committer of the Apache Airflow project. 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: MPL circuit drawer does not draw CCZ properly Take the following example: ```python from qiskit import QuantumCircuit from qiskit.circuit.library import ZGate qc = QuantumCircuit(3) qc.append(ZGate().control(2, ctrl_state='01'), range(3)) ``` The `text` and `latex` drawer outputs are the following: ```python qc.draw('text') q_0: ─■─ │ q_1: ─o─ │ q_2: ─■─ ``` ```python qc.draw('latex') ``` ![image](https://user-images.githubusercontent.com/766693/110315609-cd28db80-8009-11eb-80de-d082e1276a5b.png) However, here is the `mpl` output: ```python qc.draw('mpl') ``` ![image](https://user-images.githubusercontent.com/766693/110315793-0a8d6900-800a-11eb-9fb9-688008202f89.png) 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: channel UNC path encoding errors on windows I have some channel specifications for UNC file paths on windows that stopped working in conda 4.2.11, but did work in 4.2.9 and earlier The conda command with channel specification followed this style conda install -c file://\\machine\shared_folder\path\conda my_package Channels specified in condarc were also affected and caused a bug when parsing the condarc file (via calling a conda command). Is there another preferred style for UNC paths on windows? I see some new channel decoding code in the channel model that is likely the culprit. if value.startswith('file:') and on_win: value = value.replace('\\', '/') return Channel.from_url(value) channel UNC path encoding errors on windows I have some channel specifications for UNC file paths on windows that stopped working in conda 4.2.11, but did work in 4.2.9 and earlier The conda command with channel specification followed this style conda install -c file://\\machine\shared_folder\path\conda my_package Channels specified in condarc were also affected and caused a bug when parsing the condarc file (via calling a conda command). Is there another preferred style for UNC paths on windows? I see some new channel decoding code in the channel model that is likely the culprit. if value.startswith('file:') and on_win: value = value.replace('\\', '/') return Channel.from_url(value) 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: Argmax on empty array returns 2147483647 How to reproduce: ``` >>> jnp.argmax(jnp.array([])) DeviceArray(2147483647, dtype=int32) ``` Confirmed to occur on CPU and TPU. For reference, in numpy an exception is returned: "ValueError: attempt to get argmax of an empty sequence". 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: Upgrade style setting in upgrade_extension <!-- Welcome! Thanks for thinking of a way to improve JupyterLab. If this solves a problem for you, then it probably solves that problem for lots of people! So the whole community will benefit from this request. Before creating a new feature request please search the issues for relevant feature requests. --> ### Problem <!-- Provide a clear and concise description of what problem this feature will solve. For example: * I'm always frustrated when [...] because [...] * I would like it if [...] happened when I [...] because [...] --> The upgrade script is great. But it is missing a late complex point about style setting in `package.json` ### Proposed Solution <!-- Provide a clear and concise description of a way to accomplish what you want. For example: * Add an option so that when [...] [...] will happen --> The script should update the `package.json` file to add `style/index.js` where needed. ### Additional context <!-- Add any other context or screenshots about the feature request here. You can also include links to examples of other programs that have something similar to your request. For example: * Another project [...] solved this by [...] --> It took me some times to figure out what was wrong when replacing the official launcher when porting that alternative launcher: https://github.com/fcollonval/jlab-enhanced-launcher 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: newparallel on Windows IPython.parallel has various issues on Windows, some of which may actually be pyzmq or libzmq issues. One issue that comes up is that the Windows select does not allow events==0 (causing a crash in libzmq). This is fixed in pyzmq, with PR95: https://github.com/zeromq/pyzmq/pull/95 There also appear to be some process launching issues that result from the use of multiprocessing, which is not well behaved on Windows. 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: Tracebacks should be logged When unexpected errors occur, we currently only log the repr of the caught exception. I propose that we should begin logging tracebacks for better visibility into issues. To do so requires two steps: - begin logging caught exceptions with `logger.exception(msg)` (this will require a full audit; some caught exceptions are currently being logged as "INFO", others as "DEBUG") - in the `CloudHandler` itself, include traceback text by: ```python if record.exc_text is not None: record.message += "\n" + record.exc_text ``` 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 backoff for agent when pulling runs from Cloud In order to interface better with the `Submitted` state bottleneck, we'll implement the backoff logic for agents. As long as the agent is receiving work, it'll continue to request more work rapidly. Once work stops being delivered (either because there is no work, or there's a bottleneck), the agent will back-off requests until it reaches a 5-second steady-state interval. Note: I would recommend that we go to 10 or even 15 seconds as the steady state. That would be the maximum delay for new work to begin, but once work arrives, subsequent work would happen rapidly. ```python intervals = { 0: 0 1: 0.25, 2: 0.5, 3: 1.0, 4: 2.0, 5: 4.0 6: 8.0, 7: 15.0, } def backoff_example(): t = 0 while True: runs = get_runs_from_queue() if runs: t = 0 elif t < max(intervals): t += 1 sleep(intervals[t]) ``` 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 `--api` Flag Documentation to Prefect CLI and Docs ## Current behavior *Please describe how the feature works today* The `prefect agent start`/`prefect agent install` commands have an `--api` flag that a user can pass to specify the endpoint the agent should poll for Flow Runs. This flag used to be for internal use only, but now that Prefect Server has been open-sourced, our users find it useful as well! ## Proposed behavior *Please describe your proposed change to the current behavior* We should document this flag both in: - [ ] Our Documentation - [ ] The CLI help commands for `prefect agent start` and `prefect agent install` ## Example *Please give an example of how the enhancement would be useful* Addressed above. 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: Default ``cmake_layout()`` source folder This layout is assuming that the main library ``CMakeLists.txt`` is inside a ``src`` subfolder in the repo. This is probably not the most common user layout, in which they will have a CMakeLists.txt in the root of the folder: - How to model this? - Should we change the ``cmake_layout()`` default to ``folders.source = "."``? - Check implications of defining the root as source folder. 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: Introduce max-polls flag on all Agents ## Current behavior Currently calling `prefect agent start ...` will create a long-running process that will only stop after a kill signal is sent to the process. This is great for 99% of use cases, especially in production environments. However, there are two situations in which I'd like to specify a max number of polls that an agent will make: - **local development / short-lived agents**: sometimes when quickly iterating users spin up a local agent with many labels just to test a single run of a Flow. Doing something like `prefect agent start --max-polls 5` would allow users to kick off a single run and know the agent won't stay live - **mixed schedulers / serverless setups**: there are some situations in which we don't want to have a 24/7 process for scheduling work and instead rely on an internal-infra scheduler to check whether there's anything to do. For example, users might want to run a flow once a day within a Heroku instance, and use the Heroku scheduler to schedule a short-lived Prefect agent to run right around the time a Flow run is scheduled in Prefect Cloud. The Heroku scheduler would spin up an agent with e.g., `--max-polls 20` and their work could still be tracked via Cloud. For the latter, I fully recognize that this introduces "gotchas" but until we offer a fully serverless agent it at least exposes the pattern to users. ## Proposed behavior `prefect agent start $AGENT_TYPE --max-polls N` would only poll Prefect Cloud `N` times before gracefully exiting. For some agents, immediate exit is possible (e.g., k8s) and for others we would need to wait for submitted work to reach completion (e.g., the `LocalAgent`). Open for discussion to see what others think. 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: Update pylint to a more recent version <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues to confirm this idea does not exist. --> ### What is the expected enhancement? The version of `pylint` we are using is a bit outdated, and more recent version are available which support enhanced checks and better compatibility with recent Python versions. Updating will involve taking care of the new warnings raised and making sensible choices related to them (and might involve re-generating the .pylintrc file to take advantage of new options). See also: #1588 , #1179 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: google.cloud.logging.handlers: send messages to stderr Would it be ok if we do the print at https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/logging/google/cloud/logging/handlers/transports/background_thread.py#L222 to stderr instead? So it doesn't disturb the output of the software? Thanks 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: qiskit/mapper/_coupling.py needs more testing ### What is the expected enhancement? The coupling graph structure in `qiskit/mapper/_coupling.py` is currently not very well tested. Please, add more tests. 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: gcloud.datastore.helpers.get_value_from_protobuf() returns naive datetimes Naive datetimes (without timezones) are explicitly coerced to UTC by 'get_protobuf_attribute_and_value': ``` >>> import calendar >>> import datetime >>> import pytz >>> from gcloud.datastore.helpers import get_protobuf_attribute_and_value >>> naive = datetime.datetime(2014, 9, 16, 10, 19, 32, 4375) # no zone >>> utc = datetime.datetime(2014, 9, 16, 10, 19, 32, 4375, pytz.utc) >>> _, naive_micros = get_protobuf_attribute_and_value(naive) >>> _, utc_micros = get_protobuf_attribute_and_value(utc) >>> naive_micros == utc_micros True ``` But the datetimes returned by 'get_value_from_protobuf' do not set the UTC timezone: ``` >>> from gcloud.datastore.helpers import get_value_from_protobuf >>> from gcloud.datastore.datastore_v1_pb2 import Property >>> pb = Property() >>> pb.value.timestamp_microseconds_value = utc_micros >>> get_value_from_protobuf(pb) == utc TypeError: can't compare offset-naive and offset-aware datetimes >>> get_value_from_protobuf(pb) == naive True ``` Leaving them naive when we know they are UTC seens wrong: is there a policy in place which says we will keep in-memory timestamps around as naive-but-UTC-by-convention? 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: [feature] CMakeToolchain + Android POC Implement a proof of concept of using the new CMakeToolchain feature for building: - Android projects (from Linux/OSX) - From Windows Notes: - Android NDK can be assumed installed - Focused on creating/building 1 package, both local flow (conan install + native cmake) and ``conan create`` flow. - Integration test. - Test can be skipped for CI, but should work locally, annotate assumptions and installation details - No env-var configuration at all - All code must be private and local to the toolchains package - New cross-build model with contexts must be used if necessary, not the old os_build, arch_build - If enough time to implement reuse of a package, the ``cmake_find_package_multi`` generator must be used 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: Hide sensitive data in UI **Description** I'm using Airflow for 2 years now and I have a plugin that get password for a specific account in a Vault and then push it through a XCOM to reuse it on another tasks. The fact is that if the value is sensitive like a password, I can't hide it in the UI except for XCOM if I add an underscore in the prefix name of the key value. Eg: **kwargs['ti'].xcom_push('key':'_password', 'value':'my_value')** But for rendered template UI page, I didn't find anything similar, so if I try to pull a XCOM, it will show the value in the UI and I want to avoid it. Maybe is it possible to add a condition in **https://github.com/apache/airflow/blob/master/airflow/www/views.py** after line **635** ```python elif template_field.startswith('_'): html_dict[template_field] = ("<pre><code>sensitive data will not be exposed here</pre></code>") ``` **Use case / motivation** I know that I can use connections but in my case, and due to security politic in my company, we have to store it in a dedicated Vault. **Related Issues** N/A 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: "TypeError: decode() takes no keyword arguments" on Python 2.6 The change in commit 79c99c0 specifies the `errors` argument of `decode()` as a keyword argument. Support for keyword arguments in `decode()` was added only in Python 2.7. This causes this code to raise: ``` TypeError: decode() takes no keyword arguments ``` on Python 2.6. This occurs for example on line 2297 of [this Travis run](https://travis-ci.org/pywbem/pywbem/jobs/134314959). Specifying the `errors` argument in the `decode()` invocations in `git/objects/commit.py` as a positional argument resolves this. For example, line 504 is currently: ``` parse_actor_and_date(author_line.decode(self.encoding, errors='replace')) ``` and should be, to resolve this: ``` parse_actor_and_date(author_line.decode(self.encoding, 'replace')) ``` This applies to the three places that were changed by commit 79c99c0. I verified that the proposed change works on Python 2.6, 2.7, 3.4, 3.5. 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: pytorch_pretrained_bert/convert_tf_checkpoint_to_pytorch.py error attributeError: 'BertForPreTraining' object has no attribute 'global_step' 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: drawing `unitary` gates in mpl messed up There are huge gaps when drawing "unitary" gates. Also the box should say "unitary" (which is the `gate.name`), exactly like what latex and text drawers do. The fix should be patched on stable. ``` from qiskit import QuantumCircuit from qiskit.quantum_info.random import random_unitary circ = QuantumCircuit(2) circ.unitary(random_unitary(4), [0,1]) circ.unitary(random_unitary(4), [0,1]) circ.draw(output='mpl') ``` ![image](https://user-images.githubusercontent.com/8622381/70767542-bb398980-1d2f-11ea-8aae-b79296aeb2e1.png) 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: Allow skipping NPM download / hash checks when doing build check. ### Problem When launching a jupyterlab instance in our JupyterHub cluster, the `build_check` request can take as much as a minute despite the fact that the image that we have built is in a known-good state. ### Proposed Solution Add an option to `AppOptions` named something like `fast_build_check` (or something else; this is just a first proposal) that a user or admin can set to default to using fast build-checks (with the option at any location that calls `build_check` to override this default). I have a first cut of a solution here: https://github.com/TileDB-Inc/jupyterlab/commit/068b8e41f091e6d3a0334f1e60aeb99ee4a9ee87 but am open to changes or other approaches. 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 Qiskit/qiskit codebase. Here's the problem: circuit -> schedule raises exception <!-- ⚠ 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 ghz = QuantumCircuit(5, 5) ghz.h(0) ghz.cx(range(4), range(1,5)) ghz.barrier() ghz.measure(range(5), range(5)) sch = schedule(ghz, backend) ``` gives: AttributeError: 'NoneType' object has no attribute 'instruction_schedule_map' This works on older versions. ### 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: Schedule plot has final duration of final schedule duration even if channels are not plotted <!-- ⚠ 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**: - **Python version**: - **Operating system**: ### What is the current behavior? The domain is not adjusted if channel is dropped. ### Steps to reproduce the problem ```python import qiskit.pulse as pulse import qiskit.pulse.pulse_lib as pulse_lib sched = pulse.Schedule() sched += pulse_lib.square(1000, 1.0)(pulse.DriveChannel(0)) sched += pulse_lib.square(10, 1.0)(pulse.DriveChannel(1)) sched.draw(channels_to_plot=[pulse.DriveChannel(1)]) ``` ![image](https://user-images.githubusercontent.com/1553846/68097739-ba871b00-fe86-11e9-9ba8-5b96f904d8cf.png) ### What is the expected behavior? Adjust the domain of plot if the channel is dropped. ### 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 jupyterlab/jupyterlab codebase. Here's the problem: Extension compatibility check We need to implement a compatibility check for extensions. An idea here is to mark the packages that we depend on that should be singletons, along with the associated semver. We can then check the top level dependencies of an extension to see if they are compatible with this list, and mark it as invalid if the semver range does not overlap on any of these packages. This check requires us to vendor the Python implementation of node semver that we had previously used. 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: Meson doesn't link libgfortran when linking Fortran together with C++ I get the following linker error: cschwan@cschwan-laptop ~/projects/mwe-cpp-fortran-meson/build $ ninja -v [1/3] gfortran -Iexe@exe -I. -I.. -pipe -Wall -O0 -g -Jexe@exe -o 'exe@exe/fortran.f.o' -c ../fortran.f [2/3] c++ -Iexe@exe -I. -I.. -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -O0 -g -MMD -MQ 'exe@exe/main.cpp.o' -MF 'exe@exe/main.cpp.o.d' -o 'exe@exe/main.cpp.o' -c ../main.cpp [3/3] c++ -o exe 'exe@exe/main.cpp.o' 'exe@exe/fortran.f.o' -Wl,--no-undefined -Wl,--as-needed FAILED: exe c++ -o exe 'exe@exe/main.cpp.o' 'exe@exe/fortran.f.o' -Wl,--no-undefined -Wl,--as-needed exe@exe/fortran.f.o: In function `fortran': /home/cschwan/projects/mwe-cpp-fortran-meson/build/../fortran.f:4: undefined reference to `_gfortran_rand' collect2: error: ld returned 1 exit status ninja: build stopped: subcommand failed. with this minimal working example: [mwe-cpp-fortran-meson.tar.gz](https://github.com/mesonbuild/meson/files/1502664/mwe-cpp-fortran-meson.tar.gz) The program is basically the following callchain: `main` (written in C++) calls `fortran` (written in Fortran) calls `rand` (in the Fortran runtime library). Because the C++ linker is used to link everything together, `libgfortran` is not linked which leads to the linker error. Manually linking `libgfortran` circumvents the problem, but this specific to GCC, of course. Meson should figure out all the runtime libraries and link against 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 ipython/ipython codebase. Here's the problem: Problems due to adding IPython profile dir (~/.ipython) to sys.path When starting IPython, the profile directory gets added to sys.path. This means any `import` statement will also look for modules in that folder and in some cases allow you to import packages that aren't installed. For instance, after using the Cython magic, I can import cython even when cython is not installed in my environment. This causes issues when using packages/modules that rely on ImportError exceptions to check for optional features, for instance. We have a package that uses `cython.compiled` to check if one is using a plain-code or compiled version of a package. Due to IPython's behaviour regarding the profile directory, we cannot rely on the ImportError anymore - because `import cython` will just work. I guess IPython uses the addition to sys.path to discover extensions and such. But giving the interference with module discovery, I think different ways for this should be found. 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: Convert vendored `boltons` to a dependency ### What is the idea? `boltons 21.0.0` is now available on `pkgs/main` (and has been available on `conda-forge`). Deprecate the vendored `boltons` in favor of the latest available packages. ### Why is this needed? No need to vendor `boltons`. ### What should happen? Deprecate vendored `boltons`. 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: Patching sources tool This has been reported a few times, at least 2 publicly: - @mcraveiro: https://github.com/conan-io/conan/issues/56 - @Klaim: http://boost.2283326.n4.nabble.com/Feedback-boost-conan-binary-packages-td4682377.html I think this is a common use-case, maybe some helpers can be done to ease this task. Patching sources tool This has been reported a few times, at least 2 publicly: - @mcraveiro: https://github.com/conan-io/conan/issues/56 - @Klaim: http://boost.2283326.n4.nabble.com/Feedback-boost-conan-binary-packages-td4682377.html I think this is a common use-case, maybe some helpers can be done to ease this task. 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: Add support for c++2b and gnu++2b cpp_stds Add support for the work in progress C++23 support in GCC and Clang Signed-off-by: Joshua Ashton <joshua@froggi.es> 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: Restructure the files under algorithms.gradients. ### What should we add? Currently the files under under `algorithms.gradients` are messy. It's better to restructure the files. Grouping files by gradient type seems like a good idea. The files related to qgt and qfi are a bit tricky though. ``` gradients/ ├──base/ │ ├── base_estimator_gradient.py │ └── base_sampler_gradient.py ├── finite_diff/ │ ├── finite_diff_estimator_gradient.py │ └── finite_diff_sampler_gradient.py ├── lin_comb/ │ ├── lin_comb_estimator_gradient.py │ └── lin_comb_sampler_gradient.py ├── param_shift/ │ ├── param_shift_estimator_gradient.py │ └── param_shift_sampler_gradient.py ├── qgt/ │ ├── base_qgt.py │ ├── lin_comb_qgt.py │ └── reverse_qgt.py ├── qfi/ │ └── qfi.py └── reverse/ └── reverse_gradient.py ``` 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: AttributeError: 'NoneType' object has no attribute 'received_messages' #### Environment details OS: OS X and Linux Python 3.8.1rc1 google-cloud-pubsub==1.1.0 PubSub Emulator running out of the `google/cloud-sdk:latest` docker image #### Steps to reproduce I'm working on getting an isolated reproduction of this, but at current it's "run my integration tests against the PubSub emulator" (closed source, unfortunately) and see that on 1.1.0 the stack trace listed below gets written to stdout/stderr as it's seemingly occurring in another thread (not in my logs), and the test suite continues on normally and eventually passes. When pinned on 1.0.2, the stack trace below does not occur. For whatever it's worth, our code using PubSub via a streaming pull future has not changed recently. I get that this isn't very helpful by itself but I wanted to get report this sooner than later, instead of just pinning to 1.0.2 and forgetting about it. #### Stack trace ```python ERROR:google.api_core.bidi:Thread-ConsumeBidirectionalStream caught unexpected exception 'NoneType' object has no attribute 'received_messages' and will exit. Traceback (most recent call last): File "/Users/briancurtin/elastic/cloud/python-services-v3/.tox/integration/lib/python3.8/site-packages/google/api_core/bidi.py", line 657, in _thread_main self._on_response(response) File "/Users/briancurtin/elastic/cloud/python-services-v3/.tox/integration/lib/python3.8/site-packages/google/cloud/pubsub_v1/subscriber/_protocol/streaming_pull_manager.py", line 547, in _on_response len(response.received_messages), AttributeError: 'NoneType' object has no attribute 'received_messages' ``` 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 should allow unsetting an entrypoint `docker-compose run --entrypoint='' blah` The above command should allow you to unset the entrypoint for the container, but has no effect. The corresponding behavior was added to the docker client in https://github.com/moby/moby/pull/23718 Allow unsetting an entrypoint (resolves #5582) When an empty string is passed to the 'entrypoint' parameter, for example `docker-compose run --entrypoint='' ...` OR `docker-compose run --entrypoint '' ...` It allows the default entrypoint to be overriden by empty value. Signed-off-by: Ganesh Satpute <ghsatpute@gmail.com> docker-compose run should allow unsetting an entrypoint `docker-compose run --entrypoint='' blah` The above command should allow you to unset the entrypoint for the container, but has no effect. The corresponding behavior was added to the docker client in https://github.com/moby/moby/pull/23718 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: meson instrospect without configured directory broken by b72b5365afe319e576e254f12437aeff899eb03e Before said commit `meson introspect --buildoptions meson.build` would return something, now it returns nothing. 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: core.call_bind aggressively raises args to top trace ``` def f(a_bool, y): if a_bool: return y + 1 else: return y jax.jit(jax.remat(f), static_argnums=0)(True, 1) ``` Results in: ``` ConcretizationTypeError: Abstract tracer value encountered where concrete value is expected (in `bool`). Use transformation parameters such as `static_argnums` for `jit` to avoid tracing input values. See `https://jax.readthedocs.io/en/latest/faq.html#abstract-tracer-value-encountered-where-concrete-value-is-expected-error`. Encountered value: Traced<ShapedArray(bool[], weak_type=True):JaxprTrace(level=-1/2)> ``` I think this arises from the full_raise occurring here when processing `remat_call_p` - which raise to the JaxprTrace when we told JIT we don't want to! https://github.com/google/jax/blob/77901e9fa71f5b23066c70132a983ae57f655b39/jax/core.py#L1001 This also applies to user-defined call primitives using `core.call_bind`, resulting in unnecessary workarounds like this one in Haiku: https://github.com/deepmind/dm-haiku/blob/49b21f7192dfdb3dc0a49cc097c8d3b0ccabb107/haiku/_src/named_call.py#L101-L109 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: Do JAX jit'd Python loops run faster than jit'd LAX loop constructs? Please see the GIST [Minimal repro](https://gist.github.com/sussillo/76e191ba07bf2e75a4d4945f749549fe) where I tried to implement a recurrent computation (an echostate network) both in JAX and LAX. Using the lax.fori_loop resulted in a roughly 3x slow-down over jax jit'd naive python for loop. ``` JAX speed Params seed 100001 JAX run 0.0160 sec LAX speed LAX run 0.0418 sec ``` This is not blocking me, but I was surprised by it and I cannot find anything I did wrong, though I may have misused the APIs in some way. JAX versions are listed as comment in the gist. 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: bug in scan higher-order autodiff The test added in cf99673 shows a failing autodiff test for scan. 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: Unable to pass arguments to modules with run -m I am working with the git master branch. The following: `In [1]: %run -m my_packages.my_module -verbosity 20` returns: `UsageError: option -v not recognized ( allowed: "nidtN:b:pD:l:rs:T:em:G" )` Even though the following works: `$ python -m my_packages.my_module -verbosity 20` I am using `argparse` as follows: ``` parser = argparse.ArgumentParser(description='my_program) parser.add_argument('-verbosity', help='Verbosity', required=True); ``` 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: load checkpoint from URL Let's enable loading weights from a URL directly ## Option 1: Automate it with our current API ```python Trainer.load_from_checkpoint('http://') ``` ## Option 2: Have a separate method ```python Trainer.load_from_checkpoint_at_url('http://') ``` ## Resources We can use this under the hood: (https://pytorch.org/docs/stable/hub.html#torch.hub.load_state_dict_from_url) Any thoughts on which one is better? @PyTorchLightning/core-contributors 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: New Standard SQL Data Types Not Supported in gcloud._helpers._rows_from_json() / _CELLDATA_FROM_JSON() Standard SQL dialect support was added in 0.18.0, but current release does not support queries that return results that include data types that are not supported by Legacy SQL. E.g. executing the following query using Standard SQL: ``` SELECT PARSE_DATE('%Y%m%d', '20160810') AS table_date; ``` results in ``` rows = query.rows File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/gcloud/bigquery/query.py", line 204, in rows return _rows_from_json(self._properties.get('rows', ()), self.schema) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/gcloud/bigquery/_helpers.py", line 85, in _rows_ from_json converter = _CELLDATA_FROM_JSON[field.field_type] KeyError: u'DATE' ``` Not a significant issue since the Legacy SQL Data types will work for my needs, but wanted to report it all the same. 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: Data parameter from Operator class does not show properly in API reference ### Environment - **Qiskit Terra version**: N/A - **Python version**: N/A - **Operating system**: N/A ### What is happening? The part of the `Operator` class [API reference page](https://qiskit.org/documentation/stubs/qiskit.quantum_info.Operator.html) from `qiskit.quantum_info` in which the parameters are listed does not show properly. In particular, where the data argument is supposed to be the page reads: > Parameters or (data ([QuantumCircuit](https://qiskit.org/documentation/stubs/qiskit.circuit.QuantumCircuit.html#qiskit.circuit.QuantumCircuit)) – Instruction or BaseOperator or matrix): data to initialize operator. Instead of > Parameters data ([QuantumCircuit](https://qiskit.org/documentation/stubs/qiskit.circuit.QuantumCircuit.html#qiskit.circuit.QuantumCircuit) or Instruction or BaseOperator or matrix): data to initialize operator. However I don't see any problem with the source code: ``` def __init__(self, data, input_dims=None, output_dims=None): """Initialize an operator object. Args: data (QuantumCircuit or Instruction or BaseOperator or matrix): data to initialize operator. input_dims (tuple): the input subsystem dimensions. [Default: None] output_dims (tuple): the output subsystem dimensions. [Default: None] ``` ### How can we reproduce the issue? * Open the `Operator` class [API reference page](https://qiskit.org/documentation/stubs/qiskit.quantum_info.Operator.html). * Check the parameters section ### What should happen? You should see the aforementioned error. ### 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 google/jax codebase. Here's the problem: Cyclic references could lead to memory leaks Cyclic references (for example, in graph data structures) don't get garbage collected by python immediately. This can cause tensors to not be deallocated when all references are removed, causing memory leaks on device and possible OOM crashes. 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: Reattach ECS Task when Airflow restarts **Description** In similar fashion to https://github.com/apache/airflow/pull/4083, it would be helpful for Airflow to reattach itself to the ECS Task rather than letting another instance to start. However, instead of making this the default behavior, it would be better to use a `reattach` flag. **Use case / motivation** Allow Airflow the option to reattach to an existing ECS task when a restart happens, which would avoid having "rogue" tasks. 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: BigQuery snippets have started failing "consistently" See the 3 most recent BigQuery builds on `master`: - https://circleci.com/gh/GoogleCloudPlatform/google-cloud-python/4382 - https://circleci.com/gh/GoogleCloudPlatform/google-cloud-python/4388 - https://circleci.com/gh/GoogleCloudPlatform/google-cloud-python/4390 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: nbconvert does not process SVGs into PDFs nbconvert does not manage to take the final step to transform SVGs into PDFs and hence breaks figure inclusion in the final `pdflatex` call to generate PDF files using, for example, the --format="latex" and --format="sphinx_howto" options. This is despite the technology being ready and waiting in `IPython/nbconvert/transformers/svg2pdf.py`. (Requires `inkscape` to do the conversion.) Crucial for 1.0. By the way, I am on Mac OS but installed `inkscape` with `brew`, so the logic to choose the `Mac OS` version of `inkscape` will fail in my case. It should check if the command line `inkscape` is not already available. 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: pretty print list too slow It seems ipython's behaviour is very different if I say: ``` print range(10**6) # case 1, fraction of a second, output in ONE line range(10**6) # case 2, ten seconds, 10^6 lines ``` and the difference is not due to the actual output, but presumably the formatting of the one-value-per-line output. As this is a factor of about 10x (not counting the actual output), and growing with list size, there appears to be a problem because this is unexpected by the user. It was only through debugging, then web search, and a stackoverflow comment that I found the %pprint magic which is nowhere documented. So even if you dismiss this as bug or enhancement, this ticket should add helpful documentation. 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: Missing None verification in the CLM language modeling example Here: https://github.com/huggingface/transformers/blob/1682804ebd504d3381523116773583a52f35afd1/examples/language-modeling/run_clm.py#L230, data_args.train_file can be None (as it is checked some lines above). Therefore, there should be a check to see if it is the case or not. 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 slow in os x mavericks? I updated to mac os x mavericks yesterday and now realized that while working in ipython, it is sometimes irresponsive, i.e. I type something, but it takes ~5 seconds until it suddenly appears on the console. This issue happens more or less randomly, however more frequently when coming back to the console from another application. It seems to happen in the terminal "ipython --pylab" as well as in the qtconsole. In the normal python console it seems to be no problem. Did anyone else experience this? 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: NLLB MoE router_state referenced before assignment ### System Info - `transformers` version: 4.29.2 - Platform: Linux-5.15.0-69-generic-x86_64-with-glibc2.17 - Python version: 3.8.17 - Huggingface_hub version: 0.15.1 - Safetensors version: not installed - PyTorch version (GPU?): 2.0.1 (True) - 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?: <fill in> - Using distributed or parallel set-up in script?: <fill in> ### Who can help? @ArthurZucker @youn ### 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 ```python model = AutoModelForSeq2SeqLM.from_pretrained("facebook/nllb-moe-54b") model( input_ids=input_ids, attention_mask=attenstion_mask, decoder_input_ids=decoder_input_ids, decoder_attention_mask=decoder_attention_mask, output_router_logits=True, return_dict=True, ) ``` ```bash transformers/models/nllb_moe/modeling_nllb_moe.py", line 720, in forward outputs += (router_states,) UnboundLocalError: local variable 'router_states' referenced before assignment ``` ### Expected behavior return encoder_router_logits and decoder_router_logits rather than error. The error happens on the dense layers where no router_state is returned. 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: Improve validation schema for list_or_dict fields Right now `extra_hosts` and `labels` use "one of: object or array", but no validation is done on the contents of the `object`. I think this can be improved by creating a schema for the object that uses `patternProperties`, so that it will fail if someone uses nested objects, or arrays within the object. ``` json { "type": "object", "patternProperties": {"type": "string"}, } ``` 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: Better error message for installing JupyterLab extensions ## Description I got the following error message when installing a JupyterLab extension. It was hard for me to figure out which JupyterLab extension had caused the issue since I was building a Docker image. It would be much clearer if the name of the JupyterLab extension is included in the error message. ![image](https://user-images.githubusercontent.com/824507/75725735-f6e05180-5c95-11ea-8d40-783d17475103.png) 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: add retry policy to @asset 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: bug in np.full / lax.full for DeviceArray wrapped scalars If you pass in a jax-wrapped scalar as the fill-constant value to np.fill, it breaks, e.g.: ```python np.full((1,1), np.array([1])[0]) ``` this hits the condition in lax.full: ```python elif isinstance(fill_value, xla.DeviceValue): return FilledConstant(convert_element_type(fill_value, dtype), shape) ``` no matter what dtype is, the convert_element_type result is still a DeviceArray, then this line in lax.FillConstant: ```python class FilledConstant(xla.DeviceConstant): __slots__ = ["fill_value"] def __init__(self, fill_value, shape): assert type(fill_value) is onp.ndarray ``` wants the fill value to be an onp ndarray instead. I'm not too certain about the type logic here to make a PR confidently. 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: Circuit drawers do not handle complex values <!-- ⚠ 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**: - **Python version**: - **Operating system**: ### What is the current behavior? ```python ket = np.array([0.7071067811865476, 0, 0, 1j*0.7071067811865476]) qc = QuantumCircuit(2) qc.initialize(ket, [0, 1]) qc.draw() ``` ``` ┌────────────────────────────┐ q_0: |0>┤0 ├ │ initialize(0.70711,0,0,0) │ q_1: |0>┤1 ├ └────────────────────────────┘ ``` same for MPL <img width="221" alt="Screen Shot 2019-12-19 at 5 15 36 PM" src="https://user-images.githubusercontent.com/1249193/71214390-2da3ef80-2283-11ea-945f-6c8bc5786e96.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: Add defined phases to the PassManager <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues to confirm this idea does not exist. --> ### What is the expected enhancement? The typical (and all the preset) pass managers have fixed stages, typically something like: ``` Layout -> Routing -> Basis Translation -> Optimization Loop -> scheduling ``` We should formalize these stages, we can expand the set over time (but probably not remove) and some are obviously optional depending on runtime conditions and options and enable people to compose pass managers by constructing the phases individually and not have to worry about control flow. This also provides us the option of including hook points for backends to add customization which are backend specific before and after each transpile stage (which is something I'd like to include in #5885 ). For example, if we have a backend with all custom gate definitions our 1q optimization pass will not be able to simplify anything. But, the provider/backend author can write their own pass that runs a custom post optimization loop to do this and we update `transpile()`. 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: Function checking fails on newest sid Here's the log: ``` Running compile: Command line: ccache cc /tmp/tmp8lpdrvql.c -o /tmp/tmpnp00uh46 Code: #define lchmod meson_disable_define_of_lchmod #include <sys/stat.h> #include <unistd.h> #undef lchmod #ifdef __cplusplus extern "C" #endif char lchmod (); #if defined __stub_lchmod || defined __stub___lchmod fail fail fail this function is not going to work #endif int main () { return lchmod (); } Compiler stdout: /tmp/tmp8lpdrvql.c:13:9: error: unknown type name ‘fail’ fail fail fail this function is not going to work ^ /tmp/tmp8lpdrvql.c:13:19: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘fail’ fail fail fail this function is not going to work ^ /tmp/tmp8lpdrvql.c:13:19: error: unknown type name ‘fail’ ``` 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: Pub/Sub doc: missing/broken link for FlowControl type definition The parameter `FlowControl` in the `subscribe()` method in the ref [doc](https://googleapis.github.io/google-cloud-python/latest/pubsub/subscriber/api/client.html) doesn't have a link to its definition. We should add a link to make the doc easy to use. 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: compose should not unroll (by default) when using the circuit library   ### Information - **Qiskit Terra version**: - **Python version**: - **Operating system**: ### What is the current behavior? The idea of having a circuit library is to build up larger circuits and have simple visualizations that we can recognize when using them. I am fine having a non default option to unroll circuit when you compose it but by default the combined circuit should look like building blocks of the libraries. As an example see this figure  It should make output (by default)  @ajavadia I know we talked about this but just making issue so we remember. 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: Given inexistent file X, "%run X" reports that it's unable to open "X.py" ... which confuses users. See #13542. 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: Change --volume behavior to add instead of replace mounts Potential solution to #4728. When using the `docker-compose run` command, rather than replacing all mount when using the `-v/--volume`, this will add to the list of mounts (potentially overriding mounts already in the `docker-compose.yml` file). - [ ] Need to add unit tests `run --volumes` replaces volume configuration rather than adding Using [`run --volumes`](https://github.com/docker/compose/pull/4566) replaces all volumes in the docker-compose config. It would be more useful to me to be able to specify the volumes to mount in addition to the ones in config. Perhaps `--append-volumes` or `--add-volumes`? 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: API Endpoints - Read-only - Import errors **Description** Hello We need to create several endpoints that perform basic read-only operations on **Import error** . We need the following endpoints: - GET /importErrors - GET /importErrors/{import_error_id} For now, we focus only on read-only operations, but others will also be implemented as the next step. Detailed information is available in the issue: https://github.com/apache/airflow/issues/8118 **Use case / motivation** N/A **Related Issues** N/A 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: Commit without executing hooks If I do `index.commit(msg)` it will execute [`pre-commit`](https://github.com/gitpython-developers/GitPython/blob/d5739cd466f77a60425bd2860895799f7c9359d9/git/index/base.py#L941) and [`post-commit`](https://github.com/gitpython-developers/GitPython/blob/d5739cd466f77a60425bd2860895799f7c9359d9/git/index/base.py#L946) That makes it very hard to do the equivalent of `git commit -m "msg" --no-verify` (same as `git commit -m "msg" -n`). 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: Documentation build drops a file in the working directory ### Environment - **Qiskit Terra version**: main @ 686ba34 - **Python version**: any - **Operating system**: any ### What is happening? Running the documentation build (such as by `tox -e docs`) causes a file `new_hist.png` to be dropped in the working directory. This came from #8569, which added a `jupyter-execute` block to the `qiskit.visualization` documentation that leads a `savefig` command. ### How can we reproduce the issue? Run the documentation build. ### What should happen? No files outside the documentation build directory should be created. ### Any suggestions? The offending `.. jupter-execute` block can just be replaced by a `.. code-block` one, since it doesn't actually output anything visually, or execute code in the IPython kernel that needs persisting to later 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 conan-io/conan codebase. Here's the problem: `--build <pattern>` seems not to work When calling `conan help install` it states the following regarding the --build parameter: ``` --build=[pattern] Build always these packages from source, but never build the others. [...] 'pattern' is a fnmatch file pattern of a package name. ``` I would like to install a package and rebuild all of my own packages with it. All of my packages are within the `@monsdar/release` channel. The following seems not to work though: `conan install ... --build *monsdar*`. Conan gives me the message `ERROR: No package matching '*monsdar*' pattern`. Do I do something wrong? Or is this feature not working correctly? This happens with Conan 1.13.0 installed via Pip. Python 3.6.1 on a Windows 10 Professional with 64bit. 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: Circuit drawer reverse_bits does not reverse registerless bits ### Environment - **Qiskit Terra version**: Current main - **Python version**: 3.8 - **Operating system**: Ubuntu ### What is happening? When using classical registers only with `reverse_bits`, the registers and the bits in the registers are reversed before display. However, bits without registers are reversed in terms of usage, but are not reversed when displayed. ``` bits = [Qubit(), Qubit(), Clbit(), Clbit()] bits1 = [Clbit()] cr = ClassicalRegister(2, "cr") crx = ClassicalRegister(2, "crx") qc = QuantumCircuit(bits, cr, [Clbit()], crx, bits1) qc.x(0).c_if(crx[1], 0) qc.measure(0, bits[3]) qc.draw('mpl', cregbundle=False, reverse_bits=True) ``` ![image](https://user-images.githubusercontent.com/16268251/143066919-1730df85-81fc-49b1-bcd2-6a8a9ad9e062.png) ### How can we reproduce the issue? --- ### What should happen? Registerless bits should show in descending order. ![image](https://user-images.githubusercontent.com/16268251/143068056-abe17532-9285-420b-911e-5ba870699d27.png) ### Any suggestions? This will require the merge of #7285 before the above circuit will work. @javabster Can you assign this to 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 Lightning-AI/lightning codebase. Here's the problem: Learning Rate Schedulers' default dictionary parameters should be set via the Trainer ## 🚀 Feature The default Learning Rate Schedulers (LRS) dictionary parameters should be settable from the Trainer constructor. ### Motivation The documentation doesn't seem to be clear that the LRS have the following additional parameters available to be set when you configure the optimizers: ``` 'interval': 'epoch', # default every epoch 'frequency': 1, # default every epoch/batch 'reduce_on_plateau': False, # most often not ReduceLROnPlateau scheduler 'monitor': 'val_loss' ``` ### Pitch Set those defaults in the constructor of the Trainer and the user can set them themselves. ### Alternatives Force the return type of the function LightningModule.configure_optimizers() to be List[Optimizer], List[Dict] 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: EmailTask is outdated In `prefect.tasks.notifications`, the `EmailTask` encourages users to store usernames / passwords as Task attributes; we should be using secrets. Also, the docstring is incomplete. 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: GPT2 is not fully torch.jit.trace-able # 🐛 Bug ## Information I'm trying to use PyTorch's tracing on a pre-trained GPT2 model and running into the following warning emitted from torch.jit.trace: ``` /opt/miniconda3/envs/py3/lib/python3.6/site-packages/transformers/modeling_gpt2.py:144: TracerWarning: Converting a tensor to a Python float might cause the trace to be incorrect. We can't record the data flow of Python values, so this value will be treated as a constant in the future. This means that the trace might not generalize to other inputs! w = w / math.sqrt(v.size(-1)) ``` Additionally, if I inspect the graph generated from the trace, I can see that the denominator in that division expression is a constant value, not one determined by the size of the tensor. ## To reproduce The following snippet can be used to repro the problem (based on the example in the Quickstart guide) ```python tokenizer = GPT2Tokenizer.from_pretrained('gpt2') model = GPT2LMHeadModel.from_pretrained('gpt2').eval() example_input = torch.tensor([ tokenizer.encode("The Manhattan bridge")]) traced_model = torch.jit.trace(model, example_input) ``` ## Environment info - `transformers` version: 2.8.0 - Python version: 3.6.10 - PyTorch version (GPU?): 1.4.0 (False) 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: Feature Request to Add C17/C18/ISO-9899:2018 Support ISO-9899:2018 (C17/C18) came out last year. Although it's a non-feature corrections release, folks are going to be wanting to specify it in compiler options. As a first shot at scoping the issue, I simply hacked a local copy of mesonbuild/compilers/c.py to add 'c17', 'c18', 'gnu17', and 'gnu18' to the list of the supported standards in class GnuCCompiler, and added 'c17' and 'gnu17' in class ClangCCompiler. Passing c_std=c17 to project(), my test compiles using GCC 8 and Clang 7 were successful. There's a lot more to it than that, but maybe it won't be too tough. 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: jax.config doesn't report command-line flags correctly Another one from @jmgilmer and I - I don't think the jax config is parsing command line flags correctly. I don't know if this is functionally important or just a reporting error - but it is certainly important for user scripts knowing what flags have been set. If I run this script: ``` from absl import app, flags from jax.config import config FLAGS = flags.FLAGS def main(_): print("FLAGS.jax_enable_x64", FLAGS.jax_enable_x64) print("FLAGS.jax_debug_nans", FLAGS.jax_debug_nans) print(config.values) if __name__ == "__main__": config.config_with_absl() app.run(main) ``` I get the following problem: jax.config doesn't report the correct flag settings. ``` > python jaxtest.py --jax_enable_x64=1 --jax_debug_nans=1 FLAGS.jax_enable_x64 True FLAGS.jax_debug_nans True {'jax_enable_x64': 0, 'jax_xla_backend': 'xla', 'jax_backend_target': 'local', 'jax_platform_name': '', 'jax_device_values': 1, 'jax_debug_nans': 0, 'jax_disable_jit': 0} ``` if I run the same with envvars instead it works: ``` JAX_ENABLE_X64=1 JAX_DEBUG_NANS=1 python jaxtest.py FLAGS.jax_enable_x64 True FLAGS.jax_debug_nans True {'jax_enable_x64': 1, 'jax_xla_backend': 'xla', 'jax_backend_target': 'local', 'jax_platform_name': '', 'jax_device_values': 1, 'jax_debug_nans': 1, 'jax_disable_jit': 0} ``` I've tried parsing the flags in different ways but nothing seems to fix the 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 Lightning-AI/lightning codebase. Here's the problem: apex gradient clipping #🐛 Bug It seems when apex + gradient clipping is not handled explicitly. I see note here https://nvidia.github.io/apex/advanced.html#gradient-clipping. where amp.master_params needs to be used. Is what's in this repo correct or not? 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: Unable to set conda-build.root-dir with config Not sure the right way to do this, but it looks like there might not be any right way ATM. I would like to be able to use `conda config` to get the following added to my `.condarc` file. ```yaml conda-build: root-dir: /tmp ``` If I try to set `conda-build.root-dir` with `conda config`, I get this error. ```bash $ conda config --set "conda-build.root-dir" "/tmp" CondaValueError: Value error: Error key must be one of add_anaconda_token, shortcuts, add_pip_as_python_dependency, ssl_verify, client_tls_cert, binstar_upload, use_pip, add_binstar_token, always_copy, always_yes, client_tls_cert_key, channel_alias, changeps1, channel_priority, show_channel_urls, update_dependencies, allow_softlinks, anaconda_upload, offline, allow_other_channels, auto_update_conda, not conda-build.root-dir ``` 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: Suppress documentation logging For some reason, this line is printed many times by `generate_docs.py` when building docs: `(https://github.com/PrefectHQ/prefect/commit/7fd54f656c76aa6571939dd9b330f2a4c6867140)*</sub> 11:32:22 AM: <sub>*This documentation was auto-generated from [7fd54f6]` 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: celery worker -q --quiet seems not working with 4.4.7 Running celery 4.4.7 [not woking] Running celery 4.4.6 [ok] Running celery 4.4.1 [ok] commands : > celery -A proj worker --loglevel=info -P eventlet --quiet > celery -A proj worker --loglevel=info -P eventlet -q 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: Pylint not applied to tools directory Pylint is not applied to tools directory. Some of the tools are non-compliant with project style. 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: It should be easier to modify pass managers. <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues to confirm this idea does not exist. --> ### What is the expected enhancement? Currently, if you want to use a default pass manager with only a single pass changed, e.g. for example the swap mapper changed, you need to go and create a whole new pass manager. It should be possible to simply replace one pass in a pass manger with another. Something like: ```python pm = default_pass_manager() pm.replace(6, LookaheadSwap) # where 6 is the index of the pass in the pm ``` An index is used here since you could have multiple passes of the same type. It would also be nice to be able to slice a pm and get a new pm, e.g. `pm2 = pm[:5]` which would save people from having to rewrite things like this: ```python pass_manager = PassManager() pass_manager.property_set['layout'] = initial_layout pass_manager.append(Unroller(basis_gates)) pass_manager.append(TrivialLayout(coupling_map), condition=lambda property_set: not property_set['layout']) pass_manager.append(CheckMap(coupling_map)) pass_manager.append(DenseLayout(coupling_map), condition=lambda property_set: not property_set['is_swap_mapped']) pass_manager.append(FullAncillaAllocation(coupling_map)) pass_manager.append(EnlargeWithAncilla()) ``` 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: Figure out and documents exceptions thrown in storage.connection.Connection.create_bucket From TODO: ``` python # TODO: Which exceptions will this raise? ``` See [`storage.connection.Connection.create_bucket`](https://github.com/GoogleCloudPlatform/gcloud-python/blob/1f2aaf3606802f4f02eeb30e22e1082ef7f4594e/gcloud/storage/connection.py#L320) for relevant code and #146 for some context. `git blame` output ``` b7f1b774 (JJ Geewax 2014-01-29 18:02:29 -0500 320) # TODO: Which exceptions will this raise? ``` Figure out and documents exceptions thrown in storage.connection.Connection.create_bucket From TODO: ``` python # TODO: Which exceptions will this raise? ``` See [`storage.connection.Connection.create_bucket`](https://github.com/GoogleCloudPlatform/gcloud-python/blob/1f2aaf3606802f4f02eeb30e22e1082ef7f4594e/gcloud/storage/connection.py#L320) for relevant code and #146 for some context. `git blame` output ``` b7f1b774 (JJ Geewax 2014-01-29 18:02:29 -0500 320) # TODO: Which exceptions will this raise? ``` 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: UnboundLocalError: local variable 'seq_length' referenced before assignment ### System Info Hi, I am using the `ConvBertForTokenClassification` model in models.convbert and encountered the bug when passing only `input_embeds` to `forward()`. The traceback says that at line 833 in modeling_convbert.py ``` if token_type_ids is None: if hasattr(self.embeddings, "token_type_ids"): buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length] ``` The seq_length is unassigned. I noticed just above this piece of code in ``` elif input_ids is not None: input_shape = input_ids.size() batch_size, seq_length = input_shape elif inputs_embeds is not None: input_shape = inputs_embeds.size()[:-1] ``` seq_length is not assigned if the program enters `elif inputs_embeds is not None`. Not sure if it is the `batch_size, seq_length = input_shape` missing for `inputs_embeds` or I am not using the model correctly? ### Who can help? text models: @ArthurZucker and @younesbelkada ### Information - [ ] The official example scripts - [X] My own modified scripts ### Tasks - [ ] An officially supported task in the `examples` folder (such as GLUE/SQuAD, ...) - [X] My own task or dataset (give details below) ### Reproduction passing only `inputs_embeds` and `attention_mask` to `ConvBertForTokenClassification` model. ### Expected behavior There should be no error. 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: Extension metadata for replacement <!-- 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 Add extension metadata for replacing an extension. The system will read this metadata and disable that extension automatically. Currently extensions that replace core extensions have to tell their users to disable the core extension. This would enable that to work automatically. <!--Describe the bug clearly and concisely. Include screenshots if possible--> 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: Restrict allowed characters in connection ids ### Description I bumped into a bug where a connection id was suffixed with a whitespace e.g. "myconn ". When referencing the connection id "myconn" (without whitespace), you get a connection not found error. To avoid such human errors, I suggest restricting the characters allowed for connection ids. Some suggestions: - There's an `airflow.utils.helpers.validate_key` function for validating the DAG id. Probably a good idea to reuse this. - I believe variable ids are also not validated, would be good to check those too. ### Use case/motivation _No response_ ### 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 apache/airflow codebase. Here's the problem: Create NoAdditionalArgsInOperatorsRule to ease upgrade to Airflow 2.0 This issue is part of #8765 ## Rule Create `NoAdditionalArgsInOperatorsRule` which corresponds to > Additional arguments passed to BaseOperator cause an exception entry in UPDATING.md. This rule should allow users to check if their current configuration needs any adjusting before migration to Airflow 2.0. ## How to guide To implement a new rule, create a class that inherits from `airflow.upgrade.rules.base_rule.BaseRule`. It will be auto-registered and used by `airflow upgrade-check` command. The custom rule class has to have `title`, `description` properties and should implement `check` method which returns a list of error messages in case of incompatibility. For example: https://github.com/apache/airflow/blob/ea36166961ca35fc51ddc262ec245590c3e236fb/airflow/upgrade/rules/conn_type_is_not_nullable.py#L25-L42 **Remember** to open the PR against `v1-10-test` branch. 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: BigQuery: provide option to omit 'insertId' for 'insert_rows' and 'insert_rows_json'. Streaming inserts to BigQuery can achieve [1GB per second](https://cloud.google.com/bigquery/quotas#streaming_inserts) but only when insertId is omitted. Currently both methods from the google-cloud-bigquery [client](https://github.com/googleapis/google-cloud-python/blob/master/bigquery/google/cloud/bigquery/client.py) that implement the BigQuery insertAll REST API method, **insert_rows** and **insert_rows_json**, automatically add insertId preventing anyone from making use of the higher throughput limits. Proposing that an argument be added to one or both of these methods like "insertId=True" (defaulting to true). When false, uuid is not used to add insert IDs. Furthermore, documentation is updated to clearly articulate that omitting insertId can result in duplicate records upon retry of failed API calls according to [this guide](https://cloud.google.com/bigquery/streaming-data-into-bigquery#dataconsistency). 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: Cloud Assets: Autosynth fails to find the generated output ```bash cd asset python3 synth.py ``` Output: ``` synthtool > Ensuring dependencies. synthtool > Pulling artman image. synthtool > Cloning googleapis. synthtool > Running generator for google/cloud/asset/artman_cloudasset_v1beta1.yaml. Traceback (most recent call last): File "synth.py", line 36, in <module> artman_output_name=f"cloudasset-{version}", File "[removed]/.local/lib/python3.6/site-packages/synthtool/gcp/gapic_generator.py", line 100, in py_library return self._generate_code(service, version, "python", **kwargs) File "[removed]/.local/lib/python3.6/site-packages/synthtool/gcp/gapic_generator.py", line 183, in _generate_code f"Unable to find generated output of artman: {genfiles}." FileNotFoundError: Unable to find generated output of artman: [removed]/.cache/synthtool/googleapis/artman-genfiles/python/cloudasset-v1beta1. ``` Can you help me debug this systematically and explain your reasoning?