[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: Failed subproject dependency on systems without git shows "Git program not found." **Describe the bug** On a system where builds happen in a sandbox with **no networking** with a subproject that's a git submodule the dependency will fail with ``` ERROR: Git program not found ``` which is highly confusing because it doesn't point to the exact issue at hand. **To Reproduce** I was building gnome-usage and the error pointed at this line https://gitlab.gnome.org/GNOME/gnome-usage/-/blob/master/meson.build#L22. The archive was not retrieved with submodules which was why meson was trying to call into `git`. **Expected behavior** An error that the submodule couldn't be retrieved would be much nicer. **system parameters** * what operating system (e.g. MacOS Catalina, Windows 10, CentOS 8.0, Ubuntu 18.04, etc.) NixOS * what Python version are you using e.g. 3.8.0 3.8.5 * what `meson --version` 0.55.1 * what `ninja --version` if it's a Ninja build 1.10.1 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Remove asserts from codebase ## Welcome contributor! Asserting is perfectly fine, there's nothing wrong with it, don't get me wrong :) ... but having said that, we do want to have a more grained control over our error control strategy. As an SDK we should have an homogeneous way of dealing with invalid states, so we want to change all: ```pythnon assert(condition_is_met?) ``` ... present in the code, with: ```python if condition_is_not_met: raise QISKitError('A meaningful error message goes here') ``` **W**A**R**N**I**N**G**: Use the correct exception in every situation. We have different kind of exceptions for some of the modules, like: `QasmError`, `SimulatorError`, `ResultError`, ... all of them inherit from QISKitError. We don't throw standard exceptions!! If unsure, use `QISKitError` or ask me ;) **W**A**R**N**I**N**G**: The only part of the code where `asserting` **is allowed** (and encouraged) is on tests, so don't change asserts there :) BTW, Happy New Year!! 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: [bug] cmake_find_package generated file doesnt honor CONAN_CMAKE_SILENT_OUTPUT ### Environment Details (include every applicable attribute) * Operating System+version: not applicable * Compiler+version: not applicable * Conan version: everything released * Python version: not applicable ### Steps to reproduce (Include if Applicable) with cmake-conan at least when issuing following command: `cmake -GNinja -DCONAN_CMAKE_SILENT_OUTPUT $buildpath` and having cmake_find_package generator enabled in conanfile or passed in to conan_cmake_run(), generated Find$package.cmake has a single message() call. Since the bug is essentially here: https://github.com/conan-io/conan/blob/develop/conans/client/generators/cmake_find_package.py#L9 Same will most likely happen with calling `conan install` too.. When cmake 3.17 or never, these could be removed by filtering on the log level but that is not option for everybody. ### Logs (Executed commands with output) (Include/Attach if Applicable) Excessive output like this will be shown when generating build scripts: ```-- Conan: Using autogenerated FindXXX.cmake -- Conan: Using autogenerated FindYYY.cmake -- Conan: Using autogenerated FindZZZ.cmake ``` 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: cu3 definition in qiskit/qasm/libs/qelib1.inc is inconsistent <!-- ⚠ 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? have consistent cu3 definition. The cu3 defintion of the following file is not consistent with recent changes. https://github.com/Qiskit/qiskit-terra/blob/master/qiskit/qasm/libs/qelib1.inc https://github.com/Qiskit/qiskit-terra/commit/02e4309104d28765d598e7aee7510d75e5d6467f ### Suggested solutions update the qelib1.inc to align cu3 definition 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: Container List Fails I have a basic fig file with: ``` redis: image: dockerfile/redis ports: - "6379:6379" ``` and starting fig with `fig up -d` succeeds, however trying to list processes running throws the following error: ``` vagrant@docker:~$ fig ps Traceback (most recent call last): File "/usr/local/bin/fig", line 9, in <module> load_entry_point('fig==0.3.0', 'console_scripts', 'fig')() File "/usr/local/lib/python2.7/dist-packages/fig/cli/main.py", line 39, in main command.sys_dispatch() File "/usr/local/lib/python2.7/dist-packages/fig/cli/docopt_command.py", line 21, in sys_dispatch self.dispatch(sys.argv[1:], None) File "/usr/local/lib/python2.7/dist-packages/fig/cli/command.py", line 30, in dispatch super(Command, self).dispatch(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/fig/cli/docopt_command.py", line 24, in dispatch self.perform_command(*self.parse(argv, global_options)) File "/usr/local/lib/python2.7/dist-packages/fig/cli/command.py", line 47, in perform_command return super(Command, self).perform_command(options, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/fig/cli/docopt_command.py", line 27, in perform_command handler(command_options) File "/usr/local/lib/python2.7/dist-packages/fig/cli/main.py", line 158, in ps command = container.human_readable_command File "/usr/local/lib/python2.7/dist-packages/fig/container.py", line 89, in human_readable_command return ' '.join(self.dictionary['Config']['Cmd']) TypeError ``` 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: [DO NOT MERGE] Oslogin to pick up changes in the API or client library generator. This PR was generated using Autosynth. :rainbow: Here's the log from Synthtool: ``` synthtool > Cloning googleapis. synthtool > Running generator for google/cloud/oslogin/artman_oslogin_v1.yaml. synthtool > Ensuring dependencies. synthtool > Pulling artman image. latest: Pulling from googleapis/artman Digest: sha256:90f9d15e9bad675aeecd586725bce48f5667ffe7d5fc4d1e96d51ff34304815b Status: Image is up to date for googleapis/artman:latest synthtool > Generated code into /home/kbuilder/.cache/synthtool/googleapis/artman-genfiles/python/os-login-v1. synthtool > Replaced 'from google.cloud.oslogin.common import common_pb2' in google/cloud/oslogin_v1/proto/oslogin_pb2.py. synthtool > Replaced 'from google.cloud.oslogin.common import common_pb2' in google/cloud/oslogin_v1/proto/oslogin_pb2_grpc.py. synthtool > Cleaned up 0 temporary directories. ``` 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: Revisit iterators in storage.key, consider renaming for iterators not part of API See [note](https://github.com/GoogleCloudPlatform/gcloud-python/pull/241#discussion_r18805906) on #241 for more details. Revisit iterators in storage.key, consider renaming for iterators not part of API See [note](https://github.com/GoogleCloudPlatform/gcloud-python/pull/241#discussion_r18805906) on #241 for more details. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Client library should not try to validate sample rate The client library should allow validation of sample rate to occur on the server rather than trying to do it's own validation. Allowing the server to check errors means that we don't need to update the client if the server expands the range of sample rates that it supports. [https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/speech/google/cloud/speech/sample.py#L70][1] [1]: https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/speech/google/cloud/speech/sample.py#L70 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: Drop api_core.gapic_v1.wrap_with_paging Prefer just inlining the wrapping logic in gapic clients. /cc @landrito 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: Logging gives up too easily for non-JSON types Very possible that I'm missing a good reason why it has to be this way, but now with #1961 it's more apparent how many logging messages that seem innocuous cause issues for the current Cloud logging setup. For example, the following works fine with stdout: ``` logging.info("n = %d", np.int64(2)) INFO:root:n = 2 ``` but shows up in Prefect Cloud as ``` CRITICAL Failed to write log with error: Object of type int64 is not JSON serializable ``` Same goes for anything of type `type` which is a pretty common thing to pass via `%s` in a debugging context. Any reason we can't let `logging` do whatever it normally would to coerce these values into a printable string and then ship that? cc @joshmeek Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: NumPy 1.17 RC fails to compile with Intel C Compile 2016 <!-- Please describe the issue in detail here, and fill in the fields below --> Compiling NumPy 1.17.0rc2 sources with Intel C Compiler 2016, which does not yet implement `__builtin_cpu_supports("avx512f")` fails with compilation error: ``` icc: numpy/core/src/umath/cpuid.c numpy/core/src/umath/cpuid.c(63): catastrophic error: invalid use of '__builtin_cpu_supports' compilation aborted for numpy/core/src/umath/cpuid.c (code 1) ``` Recent Intel C compiler (2019) proceeds just fine. There is config test to probe compiler for support of `__builtin_cpu_supports`, but the the test does not discriminate between supported arguments. 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: Accessing conan trough a proxy In corperate environments it is frequently the case that internet connection must go trough a proxy server, sometimes even with authentication required. It would be good if conan would at least support the following proxy scenarios: 1. Access the internet trough a HTTP/HTTPS proxy without authentication 2. Access the internet trough a HTTP/HTTPS proxy with authentication required 3. Access the internet trough a SOCKSv5 proxy (this allows using SSH tunnels) 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: Boost rewrite breaks build Consider the following meson.build file ``` project('test_link', 'cpp', default_options : ['cpp_std=c++17']) boost_dep = dependency('boost', modules : ['system']) sources = files( 'main.cpp' ) a_out = executable('a.out', sources, dependencies : [boost_dep]) ``` (the file `main.cpp` can just contain `int main(){}`.) This no longer builds. The behavior was introduced with 08224dafcba1b694fb624553e7d84deb565aae22. The problem is that instead of `-lboost_system`, the file `/usr/lib/libboost_system.so.1.72.0` is passed as such to the linker: ``` [2/2] c++ -o a.out 'a.out@exe/main.cpp.o' -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group /usr/lib/libboost_system.so.1.72.0 -Wl,--end-group FAILED: a.out c++ -o a.out 'a.out@exe/main.cpp.o' -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group /usr/lib/libboost_system.so.1.72.0 -Wl,--end-group /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: /usr/lib/libboost_system.so.1.72.0: incompatible target collect2: error: ld returned 1 exit status ``` Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Monitoring alias package is missing new service clients https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/monitoring/google/cloud/monitoring.py is missing the new clients added to https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/monitoring/google/cloud/monitoring_v3/__init__.py Should be a relatively easy fix. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: notebook kernel dies if started with invalid parameter current git head ipython notebook --no-brow after executing any cell in a notebook the kernel dies with ``` [IPKernelApp] Bad config encountered during initialization: [IPKernelApp] Unrecognized flag: ' --no-brow' ``` seems to be related to that the parameter is the start of a valid one, completely wrong parameters (correctly) prevent the notebook from starting at all. 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: windows.compile_resources dependencies In the `meson.build` for X server, I want to write something like: ```meson convert = find_program('convert') ico = custom_target( 'xlogo-icon', command: [convert, '-background', 'transparent', '-trim', '-define', 'icon:auto-resize', '@INPUT@', '@OUTPUT@'], input: 'X.svg', output: 'X.ico', install: false, build_always: false, ) rsrc = windows.compile_resources( 'XWin.rc', # depend_files: ico, ??? # include_directories: ico.private_dir_include(), ??? ) ``` where `XWin.rc` contains an `ICON "X.ico"` line, and have correct dependencies exist. #3571 adds the depend_files: keyword, but that doesn't appear to permit a custom_target, currently There is also the problem that the directory that the custom target generates `X.ico` into needs to be added to the resource compiler's include directories: Not sure if that should be by giving the custom_target object a method to access that, or by having `compile_resources()` extract them from the dependencies... 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: STORAGE: Which requests require a project? Grepping through the JSON discovery spec for `"project"` it only occurs in ``` storage.buckets.insert storage.buckets.list ``` yet we send it with every single request: ``` python def build_api_url(self, path, query_params=None, api_base_url=None, api_version=None, upload=False): ... query_params.update({'project': self.project}) ... ``` /cc @thobrla 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: Adding `__repr__` method for the `DAGNode` object <!-- ⚠ 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. --> ### Current Behaviour There does not exist any representation method for the `qiskit.dagcircuit.dagnode.DAGNode` object as of yet ### What is the expected behavior? Just like a `Qubit` object, a `DAGNode` should be more informative and allow a user to get a basic idea about the information it contains. ### Suggested changes A `__repr__` method for the `DAGNode` which displays basic attribute information like `qargs`, `cargs` and `type` for the `DAGNode` object 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: Calling compile, transpile, or execute gives dep warning <!-- ⚠ 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? Running `compile`, `transpile`, or `execute` gives depreciation warning: ```python from qiskit import * from qiskit.transpiler import transpile IBMQ.load_accounts() backend = IBMQ.get_backend('ibmqx4') q = QuantumRegister(2) c = ClassicalRegister(2) qc = QuantumCircuit(q, c) qc.h(q[0]) qc.cx(q[0], q[1]) qc.measure(q, c) compile(qc, backend) #transpile(qc, backend) #execute(qc, backend) ``` ```python /Users/paul/Desktop/Github_repos/qiskit-terra/qiskit/transpiler/passes/mapping/barrier_before_final_measurements.py:73: DeprecationWarning: Calling ancestors() with a node id is deprecated, use a DAGNode instead our_ancestors = barrier_layer.ancestors(new_barrier_id) ``` ### Steps to reproduce the problem This appears to be caused by #1815. ### What is the expected behavior? Our own code should not give depreciation warnings. ### 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 Lightning-AI/lightning codebase. Here's the problem: Checkpoint adding "version_" at the start of the logger name **To reproduce :** ```python logger = pl.loggers.TensorBoardLogger( save_dir='.', version='my_name' name='lightning_logs' ) trainer = pl.Trainer(logger=logger, log_gpu_memory='all', max_epochs=10) ``` **Giving as a result:** - /lightning_logs/my_name: Where is saved the logs - /lightning_logs/version_my_name : Where is saved the checkpoints **Possible Explanation:** It seems like the checkpoint saving add "version_" to the start of the name even if the name have been given as a parameter : https://github.com/PyTorchLightning/pytorch-lightning/blob/3e8f2d99a9951bfb5fc67a98614128317913be1d/pytorch_lightning/trainer/callback_config.py#L52-L57 Even if in the Tensorboard Logger if the name is provided there is no "version_" prefix : https://github.com/PyTorchLightning/pytorch-lightning/blob/8b82ce09039e75f3fcb77a987c964249e38def3b/pytorch_lightning/loggers/tensorboard.py#L81 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: BUG or DOC: np.array dtype can be used to downcast data In the process of investigating the behaviour of `can_cast` for #13636 , I noticed that: ``` np.array([1000.], 'i1') # array([-24], dtype=int8) ``` i.e., casting is done unsafely. Yet the docstring suggests downcasting is not possible: ``` dtype : data-type, optional The desired data-type for the array. If not given, then the type will be determined as the minimum type required to hold the objects in the sequence. This argument can only be used to 'upcast' the array. For downcasting, use the .astype(t) method. ``` So, we should either ensure `array` behaves as documented, or document the actual behaviour. 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 group_name to AssetsDefinition.from_graph ### Issue from the [Dagster Slack](https://join.slack.com/t/dagster/shared_invite/enQtNjEyNjkzNTA2OTkzLTI0MzdlNjU0ODVhZjQyOTMyMGM1ZDUwZDQ1YjJmYjI3YzExZGViMDI1ZDlkNTY5OThmYWVlOWM1MWVjN2I3NjU) This issue was generated from the slack conversation at: https://dagster.slack.com/archives/C01U954MEER/p1655265200928469?thread_ts=1655265200.928469&cid=C01U954MEER --- ### Conversation excerpt U03BUAXQS4U: I'm using the new 'define assets from_graph' feature in 0.15.0. I can get it to work but I can't figure out how to add the created graph->asset to an asset group. It appears to get added do an asset group named 'default'. ```my_graph_asset = AssetsDefinition.from_graph(my_graph)``` graph doesn't have a group_name property, nor does from_graph(). In dagit I see my original asset group (my_asset_group) and another asset group named 'default'. my graph asset has upstream dependencies and I see the connections between my original group and the new one, so it works, but ideally I'd like to add the graph asset to the other asset group. is there a way to do this? thanks! U028M11QNDD: Hi there John. This is something we'll add within the next two releases, it was something we didn't quite have time to finish within 0.15.0. For now, one workaround you can do: ```AssetsDefinition.from_graph(my_graph).with_prefix_or_group(group_names_by_key={AssetKey("foo"): "group_name"})``` U028M11QNDD: I'll make an issue so we can track this as well: U028M11QNDD: <@U018K0G2Y85> issue add group_name to AssetsDefinition.from_graph --- #### Message from the maintainers: Do you care about this too? Give it a :thumbsup:. We factor engagement into prioritization. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Allow states in plot_histogram to be ordered by Hamming distance from target state <!-- ⚠ 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 the bit strings using in `plot_histogram` can only be ordered as ascending or descending. However, it is informative to be able to order the bit strings in terms of some distance function from a target bit string. The Hamming distance is one such measure, and is useful to see the effects of gate and environmental noise on the system as measured by number of bit flips. 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: api_core: Add metadata option to wrap_method To update GAPIC to use routing headers, `wrap_method` needs to accept more metadata than just the user agent. Example: ```python metadata = [ (b'x-google-request-params', b'name={}&book.read={}'.format(name, book.read))] self._create_book(request, retry=retry, timeout=timeout, metadata=metadata) ``` 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: Firestore: Generate Admin V1 Client. Adding the Firestore Admin API Client will allow programmatic management of indexes, and export/import operations. * Artman config: [artman_firestore_v1.yaml](https://github.com/googleapis/googleapis/blob/master/google/firestore/admin/artman_firestore_v1.yaml) Feel free to ping me if any updates are needed for the artman file. b/129353554 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: Runtime Performance Regression in `SabreLayout` ### Environment - **Qiskit Terra version**: 0.25.0 - **Python version**: 3.11 - **Operating system**: Linux ### What is happening? When running `SabreLayout` with 0.25.0 has a large performance regression between 0.24.x and 0.25.0 that is a function of the number of gates in the circuit. The rust computation of the swap map and initial layout is as fast as before, but when we iterate over that to rewrite the `DAGCircuit` using that output from rust the runtime performance is significantly slower. For more modestly sized circuits this isn't super noticeable , but as the number of instructions in a circuit increases this overhead can be significantly higher. ### How can we reproduce the issue? You can parse this qasm file from qasmbench: https://github.com/pnnl/QASMBench/blob/master/medium/bwt_n21/bwt_n21.qasm ```python from qiskit import transpile, QuantumCircuit from qiskit.providers.fake_provider import FakeCairoV2 import time import logging logging.basicConfig(level="INFO") backend = FakeCairoV2() for filename in ["bwt_n21.qasm"]: start = time.time() qc = QuantumCircuit.from_qasm_file(filename) parse_stop = time.time() print(f"parse {filename}: {parse_stop - start}") tqc = transpile(qc, backend, optimization_level=1) stop = time.time() print(f"{filename}: {stop - start}") ``` ### What should happen? The performance should be roughly equivalent to qiskit-terra < 0.25.0. Looking at 0.24.2 the above example `SabreLayout` took `22515.55800 ms` and 0.23.0 took `18759.72962 ms`. But I've been too impatient to wait for 0.25.0 to finish after several minutes. ### Any suggestions? I expect the underlying issue stems from #10366 and specifically the rust<->python boundary doing unnecessary copies or conversions when we access data as we iterate over 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 ipython/ipython codebase. Here's the problem: Security file is not removed after shutdown by Ctrl+C or kill -INT I am using IPython 0.12 (Ubuntu 11.10, Python 2.7.2+). This is how to reproduce. I just open one new notebook after starting the server. ``` % ipython profile create test [ProfileCreate] Generating default config file: u'/home/takafumi/.config/ipython/p rofile_test/ipython_config.py' [ProfileCreate] Generating default config file: u'/home/takafumi/.config/ipython/p rofile_test/ipython_qtconsole_config.py' [ProfileCreate] Generating default config file: u'/home/takafumi/.config/ipython/p rofile_test/ipython_notebook_config.py' % ipython notebook --profile=test [NotebookApp] Using existing profile dir: u'/home/takafumi/.config/ipython/profile_test' [NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8888 [NotebookApp] Use Control-C to stop this server and shut down all kernels. Created new window in existing browser session. [NotebookApp] Using MathJax from CDN [NotebookApp] Kernel started: 5946f2c5-4a2f-434f-8962-ef379d7969a0 [NotebookApp] Connecting to: tcp://127.0.0.1:42572 [NotebookApp] Connecting to: tcp://127.0.0.1:39724 [NotebookApp] Connecting to: tcp://127.0.0.1:54142 [IPKernelApp] To connect another client to this kernel, use: [IPKernelApp] --existing kernel-5946f2c5-4a2f-434f-8962-ef379d7969a0.json --profile test ^C % ls ~/.config/ipython/profile_test/security/ kernel-5946f2c5-4a2f-434f-8962-ef379d7969a0.json ``` BTW, is it safe to do `rm ~/.config/ipython/profile_*/security/*` when there is no IPython instance running? 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: whos under pypy1.6 magic who command works, but 'whos' gives an error that has to do with numpy /IPython/core/magic.py in magic_whos(self, parameter_s) line 870 AttributeError: 'module' object has no attribute 'ndarray' This version of pypy has a trial version of numpy that only has 1d arrays, not ndarray. 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: to_arrow() method similar to to_dataframe() Current there's a `to_dataframe()` method that returns a pandas `DataFrame` from a query. `DataFrame`s don't efficiently support array and struct values, but `pyarrow` provides efficient support for them: ```python In [11]: import pyarrow as pa In [13]: a = pa.array( ...: [ ...: {'a': [1, 2, 3]} ...: ], ...: pa.struct([pa.field('a', pa.list_(pa.int64()))]) ...: ) In [14]: a Out[14]: <pyarrow.lib.StructArray object at 0x7f55f8764b88> [ {'a': [1, 2, 3]} ] ``` A `to_arrow()` method will make it easier to efficiently support more complex types going forward in downstream libraries like [ibis](https://github.com/ibis-project/ibis). 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 support for `Expr` values to `DAGCircuit.replace_block_with_op` ### What should we add? This may follow easily from the work in #10226, but at the very least this issue requires additional tests to be written to verify that the function is working as expected. Depends on #10223, #10224. 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: A form of conan remote list that can be used with conan config install See https://github.com/conan-io/docs/issues/697 for further discussion/motivation, but basically the idea is that the output of `conan remote list` is not compatible with the format of `remotes.txt` expected for use with `conan config install`. It could be nice to have a modified version of `conan remote list` (@memsharded has suggested `conan remote list --raw`) so that ```bash conan remote list --raw > remotes.txt ``` can conveniently format a user's remotes for use in a packaged Conan client config. 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: Ability to provide sample conf JSON for a dag in trigger page **Description** In the trigger page, there is a text area to enter (optional) conf json. It would be great if a sample JSON can be provided programatically while defining DAG **Use case / motivation** This will improve usability of the UI that triggers a DAG Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: CMake toolchain file does not define CMAKE_C*_COMPILER_ABI **Describe the bug** meson fails to find cmake dependencies on Linux with x32 ABI. It appears to be caused by toolchain file created by meson which contrary to CMake own mechanism does not set compiler's ABI ie CMAKE_C_COMPILER_ABI or CMAKE_CXX_COMPILER_ABI. and at the same time sets CMAKE_C*_COMPILER_FORCED. **To Reproduce** Any meson file with cmake dependency, however cmake file needs to be in /usr/libx32/cmake directory. **Expected behavior** cmake dependency should be found **system parameters** * Plain build * PLD Linux (arch x32) * Python 3.8.7 * meson 0.56.2 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Have RAG return generator cross-attentions when output_attentions=True # 🚀 Have RAG return generator cross-attentions when output_attentions=True This feature request is for the RAG code to be modified so that if `output_attentions=True`, it returns the generator's cross-attentions in addition to the attentions it already returns. ## Motivation I'm interested in extracting the generator's attentions from a RAG generator model. Currently, `transformers` allows you to extract the generator's encoder attentions and decoder attentions, but not it's cross attentions. For example, inside `modeling_rag.py`, the return objects such as [RetrievAugLMMarginOutput](https://github.com/huggingface/transformers/blob/master/src/transformers/models/rag/modeling_rag.py#L38), have fields for these other attentions, but not the cross-attentions. Because both T5 and BART can output cross-attentions, I think they could simply propagate up through the RAG code. Is there a reason this isn't already the case? Or could I do a PR to include the cross attentions along with the other attentions in the model output? ## Your contribution On my own fork of `transformers`, I've already added this feature and would happily submit a PR! Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: records.fromfile - 64 bit incompatibility Hello, https://github.com/numpy/numpy/blob/983bbb5ed2495e034b437a0b58a69371d4dfed74/numpy/core/records.py#L796 Seems like unfortunately numpy.core.records.fromfile method uses 32 bit integers. Makes it impossible to read data larger than 4GB. Python 3.7.1 64 bit numpy 1.15.4 (numpy-1.15.4-cp37-none-win_amd64.whl) call: `raw_data = numpy.core.records.fromfile(io_input, shape=420453029, offset=0, formats='i4,u4,i4', names='t,k,n', byteorder='<')` 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: 'load_table_from_dataframe' raises OSError with STRUCT / RECORD columns. pyarrow-0.14.0 pandas '0.24.2' windows 10 Hi, I am tring to load dataframe to big query that looks like that ``` uid_first agg_col 1001 [{'page_type': 1}, {'record_type': 1}, {'non_consectutive_home': 0}] ``` the agg_col is list of dicts I also tried dict Schema config: ``` schema = [ bigquery.SchemaField("uid_first","STRING",mode="NULLABLE"), bigquery.SchemaField("agg_col","RECORD",mode="NULLABLE",fields=[ bigquery.SchemaField("page_type", "INTEGER", mode="NULLABLE"), bigquery.SchemaField("record_type", "INTEGER", mode="NULLABLE"), bigquery.SchemaField("non_consectutive_home", "INTEGER", mode="NULLABLE")])] ``` load command ``` dataset_ref = client.dataset('dataset') table_ref = dataset_ref.table('table') table = bigquery.Table(table_ref,schema=schema) table = client.load_table_from_dataframe(dff, table).result() ``` The error message ``` Traceback (most recent call last): File "<ipython-input-167-60a73e366976>", line 4, in <module> table = client.load_table_from_dataframe(dff, table).result() File "C:\ProgramData\Anaconda3\envs\p37\lib\site-packages\google\cloud\bigquery\client.py", line 1546, in load_table_from_dataframe os.remove(tmppath) FileNotFoundError: [WinError 2] The system cannot find the file specified: 'C:\\Users\\ADMINI~1\\AppData\\Local\\Temp\\tmpcxotr6mb_job_5c94b06f.parquet' ``` 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: duplicate log messages Adding code ```python class DbgViewHandler(logging.Handler): def emit(self, record): print("DbgViewHandler: %s" % record) logger = logging.getLogger("logging_test") logger.setLevel(logging.DEBUG) logger.propagate = False stream_handler = logging.StreamHandler() stream_handler.setLevel(logging.WARNING) # all going to stderr dbgview = DbgViewHandler() # all going to stdout dbgview.setLevel(logging.DEBUG) logger.addHandler(dbgview) logger.addHandler(stream_handler) logger.info("Hello there") logger.warn("Whoa there") ``` To the bottom of conda/gateways/logging.py outputs too many copies of 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 Qiskit/qiskit codebase. Here's the problem: CSPLayout is biased towards "low" qubits Take the following example: ```python from qiskit import QuantumCircuit qc = QuantumCircuit(3) qc.cz(0, 1) qc.cz(1, 2) qc.draw() ``` If this circuit is laid-out in a 5-qubit linear coupling map, using `CSPLayout`, the result is the following: ```python from qiskit.transpiler import CouplingMap from qiskit.converters import circuit_to_dag from qiskit.transpiler.passes import CSPLayout coupling_map = CouplingMap.from_line(5) dag = circuit_to_dag(qc) pass_ = CSPLayout(coupling_map) pass_.run(dag) print(pass_.property_set['layout']) ``` ``` Layout({0: Qubit(QuantumRegister(3, 'q'), 0), 1: Qubit(QuantumRegister(3, 'q'), 1), 2: Qubit(QuantumRegister(3, 'q'), 2)}) ``` Notice that there are other possible layout allocations besides the trivial one here. However, `CSPLayout` always choose this one, even when `CSPLayout(..., seed=...)` is set. ### What is the expected enhancement? I would expect a uniformly distribution of all possible allocations, controlled by the seed parameter. 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: classical_function creates wrong circuits for some cases ### Information - **Qiskit Terra version**: master - **Python version**: 3.8 - **Operating system**: macOS Catalina ### What is the current behavior? `classical_function` creates wrong circuits for some cases. I confirmed at least two cases. ### Steps to reproduce the problem Case 1) ``` def expr1(x1: Int1, x2: Int1, x3: Int1) -> Int1: return x1 cf = classical_function(expr1) print(cf.synth()) q_0: ──■── │ q_1: ──┼── │ q_2: ──┼── ┌─┴─┐ q_3: ┤ X ├ └───┘ ``` Case 2) ``` def expr2(x1: Int1, x2: Int1, x3: Int1) -> Int1: return x1 or x2 or x3 cf = classical_function(expr2) print(cf.synth()) q_0: ──o──────────── │ q_1: ──o────o─────── │ │ q_2: ──■────■────■── ┌─┴─┐┌─┴─┐┌─┴─┐ q_3: ┤ X ├┤ X ├┤ X ├ └───┘└───┘└───┘ ``` ### What is the expected behavior? Case 1) The control bit of the CNOT gate should be the most bottom bit. As written in the [documentation](https://qiskit.org/documentation/apidoc/classicalfunction.html), following Qiskit’s little-endian bit ordering convention, the left-most bit (x1) is the most significant bit and the right-most bit (x3) is the least significant bit. The following code is an example for the correct bit ordering. ``` def expr3(x1: Int1, x2: Int1, x3: Int1) -> Int1: return not x1 and x2 and x3 cf = classical_function(expr3) print(cf.synth()) q_0: ──■── │ q_1: ──■── │ q_2: ──o── ┌─┴─┐ q_3: ┤ X ├ └───┘ ``` Case 2) The circuit does not represent `x1 or x2 or x3`. For example, when (x1, x2, x3) = (001), $q_3$ of the circuit does not become 1. ### 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 numpy/numpy codebase. Here's the problem: Going from numpy 1.14.5 to 1.15.0rc1 breaks loading a DLL using ctypes In our [Python API](https://github.com/ni/nimi-python) for accessing measurement hardware we allow the customer to retrieve their measurements in `numpy` arrays in case they want to do additional processing. When using `numpy` 1.14.5 or earlier, we are able to load our C DLL with no issue and make the appropriate calls using `ctypes`. When using `numpy` 1.15.0rc1, we get an error when `ctypes` tries to load the DLL saying "[WinError 126] The specified module could not be found". I am using `tox` to run tests so it is using `venv` and all I have to do is change the version of `numpy` and it will start working. This means the DLL is in the path as expected and all dependencies are also loadable. I have verified that `numpy` is the only installed package whose version is changing. I have verified that the path environment variable has the appropriate directory even in the failure case. I have verified that this happens on Python 2.7 and 3.6, both 32 bit and 64 bit. As far as I know we are using `ctypes` correctly. At this point I don't have any more ideas on what to look at. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: Support thin archives for static libraries that are not installed I have a project which generates several executables which (partially) share the same source files. Since each executable is first compiled in its own subdirectory, all these shared source files are recompiled for every executable. This is undesirable if I know that identical object files will be produced (that is, the compiler options are identical). Is there a way to specify the name of the build-subdirectory to avoid this repeated redundant compilation? I am aware that one could use static libraries to work around this problem, but besides being overkill this also has several disadvantages: It also has the overhead of building the library, and moreover, to support e.g. proper support for LTO it requires linker plugins etc. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: ma.average ignores masked weights The np.ma.average function ignores masked weights. Averaging a masked array with unmasked and masked weights incorrectly gives the same result. I am using numpy version 1.13.3, python 2.7.12. In previous versions of numpy (e.g. 1.11.0b3) ma.average did not exhibit this behavior. ``` import numpy as np import numpy.ma as ma x = np.ma.array(np.arange(9).reshape(3, 3), mask=[[1, 0, 0], [1, 0, 0], [0, 0, 0]]) w=ma.masked_array([31,28,31],mask=False) w2 = ma.masked_array([31,28,31],mask=[1,0,0]) ``` ``` np.ma.average(x, axis=0, weights=w, returned=True) (masked_array(data = [6.0 4.0 5.0], mask = [False False False], fill_value = 1e+20) , array([ 31., 90., 90.])) np.ma.average(x, axis=0, weights=w2, returned=True) (masked_array(data = [6.0 4.0 5.0], mask = [False False False], fill_value = 1e+20) , array([ 31., 90., 90.])) ``` 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: Use WebSocket.ping to keep connections alive across proxies I am accessing a remote IPython Notebook and need to use a proxy (Squid/SOCKS) for internet access. As long as I am running cells everything works fine, but after one minute of inactivity the proxy seems to close the connection, resulting in the following Firefox console log: ``` The connection to wss://example.org/kernels/$uuid/shell was interrupted while the page was loading. @ https://example.org/static/js/kernel.js ``` The websocket connection is reestablished immediately (and interrupted again after one minute), but running cells does not work anymore until I manually restart the kernel. ``` ipython --version 0.13.1.rc2 ``` Sending any message via each websocket (shell+iopub) will avoid interruption. This is a quick and _dirty_ client side workaround: ``` from IPython.core.display import HTML HTML('''<script> var keepalive_timer; function keep_connection_alive() { IPython.notebook.kernel.execute(); keepalive_timer = setTimeout('keep_connection_alive()', 55000); } keep_connection_alive(); </script>''') ``` WebSocket has ping and pong frames for keep-alive, tornado has a ping() function to send such a frame. Could the ping function be called somewhere in the kernel code to keep alive connections even via proxy? 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] Add option to delete necessary files / directories when running conan config install An issue that I've run into is that restructuring the structure of Conan profiles in a shared Conan configuration via Git can fail when switching a file to a directory of the same name or vice versa. This pretty much fails without explanation, so the error message should probably be improved. Perhaps it would be best to make this default behavior, which wouldn't require anything special to ensure scheduled runs of `conan config install` don't break. Otherwise, there could be an option like `--force` which would all overwriting any conflicting directories / files. To reproduce this issue: 1. Create a git repository to share Conan configuration through `conan config install`. ``` mkdir conan-config cd conan-config mkdir profiles mkdir -p profiles/debug touch profiles/debug/address-sanitizer git init git add -A git commit -m "Initial commit" ``` 2. Install the repository using `conan config install`. ``` conan config install . ``` 3. Now re-organize such that a directory is now a file in the `conan-config` repository. ``` mv profiles/debug/address-sanitizer profiles/address-sanitizer rmdir profiles/debug touch profiles/debug git add -A git commit -m "Restructure profiles" ``` 4. Re-run `conan config install` to update the profiles. ``` conan config install Config install: /var/home/jordan/Projects/test/conan-config Copying file address-sanitizer to /var/home/jordan/.conan/profiles Copying file debug to /var/home/jordan/.conan/profiles ERROR: Failed conan config install: ``` Note the vague error message. - [X] I've read the [CONTRIBUTING guide](https://github.com/conan-io/conan/blob/develop/.github/CONTRIBUTING.md). Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: get_variable with a file object as default value: Argument of type File is not held by an ObjectHolder **Describe the bug** After updating Meson, I see this error in a previously working build: ``` build/analysis/vale/meson.build:24:0: ERROR: Argument build/analysis/vale/vale-styleguide/config/documentation.vale.ini of type File is not held by an ObjectHolder. This is a Meson bug and should be reported! ``` The file is being specified in this manner: ``` # Supply a style file, which will use this file instead of the default .vale.ini vale_config_file = get_variable('vale_config_file', files('vale-styleguide/config/documentation.vale.ini')) ``` The default variable option is being used - I'm not overriding it. The same is happening in a Doxygen module I use: ``` doxyfile_input = get_variable('doxyfile_input', files('Doxyfile.in')) ``` I tried moving the file object into another variable: ``` vale_default_config_file = files('vale-styleguide/config/documentation.vale.ini') vale_config_file = get_variable('vale_config_file', vale_default_config_file) ``` With teh same result - the error is reported on the `get_variable` line. **system parameters** * Is this a [cross build](https://mesonbuild.com/Cross-compilation.html) or just a plain native build (for the same computer)? **native** * what operating system (e.g. MacOS Catalina, Windows 10, CentOS 8.0, Ubuntu 18.04, etc.) **MacOS 10.15.7** * what Python version are you using e.g. 3.8.0 **Python 3.9.6** * what `meson --version` **0.59.0.rc1** 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: clbit_labels should not contain null <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Information The definition of `clbit_labels` was changed in #879 by @dcmckayibm. It used to be something like: ```[["c", 2], ["d", 3]] ```, which assigns contiguous regions of memory to each register. Now it is like this, where single classical bits can be assigned to arbitrary locations of memory. ```[["c", 1], ["c", 0], ["d", 0], ["d", 2], ["d", 1]]``` I agree with this change. However, the schema currently also allows something like this for `clbit_labels`. ```[["c", 1], ["c", 0], ["d", 0], ["d", 2], ["d", 1], null, null]``` I don't think the schema should allow this. I want to have a convention that for each experiment, `memory_slots` defines the total amount of classical (slow) memory bits for that experiment, and `clbit_labels` have a 1-1 correspondence with those. It is fine for `qubit_labels` to have null, as the device can have more qubits than used for an experiment. But `clbit_labels` should just be as many classical bits as the experiment uses. By the way this information is important for Terra to be able to rebuild the original circuit registers in the Result. 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 setuptools to dagster/setup.py install_requires `setuptools` isn't a part of core Python, so when installing Dagster into an isolated environment by a package manager (e.g. PDM, poetry), it will not get picked up and installed as a dependency. Here's where it's throwing a `ModuleNotFoundError` when I try to run `dagster-cloud agent run`: https://github.com/dagster-io/dagster/blob/96a6762095eec173d9ec3a524dd64382d34f5ed7/python_modules/dagster/dagster/core/definitions/utils.py#L7 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 optional stdout logging for tasks ## Current behavior Currently, `print` statements or any other stdout is not treated in any special way. This has two consequences: - users who use `print` statements locally and can see the output are surprised when the output doesn't appear in the Cloud logs - print statements from third-party libraries that might be useful are not surfaced in cloud execution ## Proposed behavior We should introduce a new keyword argument on all Tasks `log_stdout` which defaults to `True`. When `True`, all standard out is converted to a DEBUG level log. When toggled to `False`, we will not redirect. This will capture richer information from task runs, but also allow for incredibly simple logging for our less advanced users: ```python @task def example(): print('hi') print('this is a test') print('of our emergency broadcast system') ``` will result in 3 debug logs. ## Example This is actually very simple with Python builtins: ```python import prefect from contextlib import redirect_stdout class RedirectToLog: def write(self, s): # avoids blank newlines if s.strip(): prefect.utilities.logging.prefect_logger.debug(s) to_debug_log = RedirectToLog() with redirect_stdout(to_debug_log): print('hi') print('this is a test') print('of our emergency broadcast system') ``` results in : ``` [2020-02-17 00:02:13,642] 4-- DEBUG - prefect | hi [2020-02-17 00:02:13,642] 4-- DEBUG - prefect | this is a test [2020-02-17 00:02:13,643] 4-- DEBUG - prefect | of our emergency broadcast system ``` **NOTE:** In our case, we want want to generate the redirect class on the fly so that it uses the task run specific logger in each case. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Auto-suggestion (matching brackets code maybe ?) creates broken code even on trival statements This is in a fresh `python:latest` docker container where I installed the latest ipython version with pip. ``` Python 3.10.1 (main, Dec 21 2021, 09:01:08) [GCC 10.2.1 20210110] Type 'copyright', 'credits' or 'license' for more information IPython 8.0.0 -- An enhanced Interactive Python. Type '?' for help. In [1]: foo = 'bar'' ``` I typed `foo = 'bar'` and it added a second single quote at the end, which is obviously invalid. The same happens with double quotes, so as much as I dislike this black integration, it seems unrelated since it happens at input time and not only when I run the code. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Notebook: Long delay before closing/server stop on Windows I'm on Windows with ipython 2.4.0 The console says "Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).". But doing so takes over a minute on my machine to actually exit! Just measured and it was 102 seconds. It's faster to just kill python.exe. Which is ugly and can't be the expected behavior. This is not new for me, but I couldn't find related issues, so what's up with that? 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: Compile Cython code to C++ Meson 0.59.0 introduced native support for [Cython](https://mesonbuild.com/Cython.html#cython). I am trying to compile an existing Cython project using Meson. The Cython code relies on functionality from the C++ standard library and therefore must be compiled to C++. I found some discussion on whether compilation from Cython to C++ can be supported in pull request #8706. Unfortunately, it remains unclear to me whether this functionality is already supported or not. Is it possible to compile `.pyx` files to `.cpp` files using Meson? Either by globally defining the target language in the `meson.build` file, or by adding the compiler directive `# distutils: language = c++` to the `.pyx` files. I tried the latter, but Meson still produces `.c` files. 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.xla_computation ignores its static_argnums argument The implementation of jax.xla_computation completely ignores its static_argnums argument, which seems like an oversight. 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: Double-dash becomes en-dash in docs for "cd" magic The double-dash in [this line][line] gets rendered as an en-dash (Unicode U+2013) in [the docs][docs] for the `cd` magic. I don't know how to fix it, sorry, otherwise I'd submit a pull request :frowning_face: [line]: https://github.com/ipython/ipython/blob/86d24741188b0cedd78ab080d498e775ed0e5272/IPython/core/magics/osm.py#L317 [docs]: https://ipython.readthedocs.io/en/stable/interactive/magics.html#magic-cd 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.scipy.ndimage.map_coordinates round half is different than scipy `jax.scipy.ndimage.map_coordinates` implements 'round half to even' when using nearest-neighbor interpolation and the coordinat values are exactly half (i.e. both 1.5 and 2.5 get rounded to 2). This is the default behavior for jax and ordinary numpy rounding (round, around, rint). However scipy.ndimage.map_coordinates appears to implement 'round half up'. The difference between jax and scipy is illustrated with the following commands. `>>> x = np.arange(10).astype(np.float32)` `>>> coords = [[3.5, 4.5, 5.5, 6.5, 7.5]]` `>>> jax.scipy.ndimage.map_coordinates(x, coords, order=0)` `DeviceArray([4., 4., 6., 6., 8.], dtype=float32)` `>>> scipy.ndimage.map_coordinates(x, coords, order=0)` `array([4., 5., 6., 7., 8.], dtype=float32)` Not sure which behavior is desired, but if the default numpy behavior is desired, the jax.scipy documentation should mention this. If the scipy behavior is desired, the rounding function at [https://github.com/google/jax/blob/7d157c71815e5386f2b449bac69ef9e3ab7e701f/jax/scipy/ndimage.py#L40](https://github.com/google/jax/blob/7d157c71815e5386f2b449bac69ef9e3ab7e701f/jax/scipy/ndimage.py#L40) should be changed to something like: `index = jnp.floor(coordinate + .5).astype(jnp.int32)` 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: Allow installation of output header (-H) for Vala library targets Currently it is unconditionally named after the library itself, but this is not always what people want. For instance in #890, @grindhold names the library `libhttpseverywhere-0.2`, but the header is called `libhttpseverywhere.h`. Found while investigating #890 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_project_arguments should ensure it is called before build targets only in the current project, not subprojects If a subproject is defined, and `add_project_arguments` is called after said subproject, then meson will error out with ``` Tried to set project arguments after a build target has been declared. This is not permitted. Please declare all project arguments before your targets. ``` This doesn't seem correct, as `add_project_arguments` differese from `add_global_arguments` specifcially in that it doesn't affect subprojects. Specfically this is annoying because it means that if a dependency needs to add define as an argument rather than as configuration_data that must be done before the subproject, making it impossible to use the fallback parameter. 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: Error differentiating QR decomposition This appears to be a bug but unfortunately I don't have time to delve into it. Below is a simple script to do gradient descent on a function involving a QR decomposition. It fails when I execute `training_gradient_fun` with `TypeError: No abstraction handler for type: <class 'jax.ad_util.Zero'>`. Ubuntu 16.04 python 3.6.6 jax 0.1.20 jaxlib 0.1.9 ``` import jax import jax.numpy as np import numpy as onp def loss(weights, inputs): q, r = np.linalg.qr(weights) a = np.matmul(q, weights) return np.mean(a ** 2) training_gradient_fun = jax.jit(jax.grad(loss)) inputs = onp.random.rand(5, 5) weights = onp.random.rand(5, 5) for i in range(100): weights -= 0.1 * training_gradient_fun(weights, inputs) ``` 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: Don't pass ConanFileReference object to conan_api, pass string https://github.com/conan-io/conan/pull/5176/files introduces a ConanFileReference via the conan_api, please fix. 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: Pulse and Schedule plots do not start at t0=0 <!-- ⚠ 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? As noted in https://github.com/Qiskit/qiskit-terra/pull/3418#pullrequestreview-313349295, the pulse and schedule plots do not start at t=0, nor do they finish at `t=t0+duration` ### 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.constant(10, 1.0)(pulse.DriveChannel(1)) sched.draw(channels_to_plot=[pulse.DriveChannel(1)]) ``` ### What is the expected behavior? They should start and stop at t0(duration) ### Suggested solutions Any ideas @nkanazawa1989? 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: Filename completion with quotes in filename does not escape the quotes When completing filenames containing quotes those are completed verbatim, closing the string. The user has to go back in the string to escape the quotes manually. ``` $ touch /tmp/foo\'bar $ ipython In [1]: open('/tmp/foo<TAB> # actual In [1]: open('/tmp/foo'bar # Expected: In [1]: open('/tmp/foo\'bar ``` ```python {'commit_hash': '3a3686a', 'commit_source': 'repository', 'default_encoding': 'UTF-8', 'ipython_path': '/home/t-8ch/Projekte/ipython/IPython', 'ipython_version': '6.0.0.dev', 'os_name': 'posix', 'platform': 'Linux-4.8.10-1-ARCH-x86_64-with-arch', 'sys_executable': '/home/t-8ch/.local/share/virtualenvs/ipython/bin/python', 'sys_platform': 'linux', 'sys_version': '3.5.2 (default, Nov 7 2016, 11:31:36) \n[GCC 6.2.1 20160830]'} ``` 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: make docs failing https://github.com/huggingface/transformers/blob/2a606f9974feb0f7578e6a638c7e5b548523ecb4/CONTRIBUTING.md?plain=1#L211-L221 ```bash make docs cd docs && make html SPHINXOPTS="-W -j 4" Application error: config directory doesn't contain a conf.py file (source) make[1]: *** [html] Error 2 make: *** [docs] Error 2 ``` transformers version: master branch @sgugger 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: [bug] Can't call `conan upload --recipe-only` twice with backup sources enabled ### Steps to reproduce 1. Enable backup sources 2. Export a recipe that downloads file 3. Call conan upload only recipe for ref 4. Do it again, it fails due to KeyError Found while prepping for https://github.com/conan-io/conan-center-index/pull/18082 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: interactive -i mode doesn't work after exceptions since 4.1.1 Hi, I recently noticed that after upgrading from 4.0.3 to 4.1.1 (from anaconda), `-i` flag no longer drops to the interactive shell but quits after an exception. I downgraded to 4.0.3 and it is now working correctly. I searched on google but couldn't find a similar issue. Any ideas? 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: Remove deprecated `conda.install` ### What is the idea? Remove clearly deprecated code. ### Why is this needed This submodule was deprecated 4 years ago. ### What should happen? Remove `conda.install` and associated code that is no longer in use. ### Additional Context _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 mesonbuild/meson codebase. Here's the problem: Default value of UserFeatureOption is `enabled` instead of `auto` According to `meson --help`: ``` --auto-features {enabled,disabled,auto} Override value of all 'auto' features (default: auto). ``` However, in reality the default value is `enabled`. We should fix it to be `auto`. 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: Check release is broken on main <!-- Welcome! Thank you for contributing. These HTML comments will not render in the issue. 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 <!--Describe the bug clearly and concisely. Include screenshots if possible--> Check release is broken on main The reason that the package on main are targeted 4.1.0 prereleases but the version have not been bumped. 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: metrics.sklearns don't work with DDP: Tensors must be CUDA and dense ## 🐛 Bug Using sklearn-like metrics (from metrics.sklearns) works fine in DP mode, but results in the following error in DDP mode: `Tensors must be CUDA and dense` ### To Reproduce This colab notebook has a full example: https://colab.research.google.com/drive/1uxihs4pztF_qTN-gkO1QOaX0npzE_uSZ?usp=sharing Mentioning @justusschock 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 informative error message when the argument "shots" passed to the execute function is not of type int <!-- ⚠ 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? execute(circuit, backend = Aer.get_backend('qasm_simulator), shots = "1024") doesn't give an informative error message (Issue number 842 in qiskit-aer). Add an informative error message. This isssue was posted in qiskit-aer which is a wrong place for it. Creating a new issue at qiskit-terra (which is relevant to it) and creating a pull request for a solution Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the numpy/numpy codebase. Here's the problem: BLD: warning "document not included in any toctree" while building documentation When building documentation, there are many tens of warnings `WARNING: document isn't included in any toctree`. It seems to be from class attribute `autoattribute` generated documentation. This might be a numpydoc issue, but it does not occur when building scipy documentation. Any hints where to debug 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 ipython/ipython codebase. Here's the problem: make zmq-console and qtconsole monitor activity they did not initiate over at ivanov/vim-ipython#31, @pielgrzym pointed out that vim-ipython is able to monitor and display input and output for the kernel it is monitoring, regardless of what client initiated this activity, whereas activity initiated from vim-ipython is not reflected by these clients. This is not unique to vim-ipython, however. Both the qtconsole and console frontends currently ignore the messages that they did not initiate. In other words, if you have two qtconsoles connected to the same kernel, executing code from one of them will not affect the other one in any way. It would be nice for the qtconosle and console frontends to periodically check the relevant channels and make this activity visible. This would certainly be a good candidate for toggle-able behavior, since sometimes you really do want to ignore what other clients are doing. 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: Remove Textbook reference from Phase Estimation docstring ## Description This line refers to the Qiskit Textbook as a reference for phase estimation. This page is no longer maintained and we should remove the reference https://github.com/Qiskit/qiskit-terra/blob/c8552f6b51a36aa432b21b0d31b88e212a104ca7/qiskit/circuit/library/phase_estimation.py#L46 CC: @abbycross, @lerongil, @javabster 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: `flow.run()` crashes on scheduled states in the far future ## Description *A clear description of the bug* `Paused` states default to setting a future run time in the far future; this exceeds the maximum argument that can be provided to `time.sleep()`. This crashes `flow.run()` when hitting a pause state. To be clear, Pausing and `flow.run()` aren't a great combo because there's not a way to provide a `Resume` state, but we can solve the crash. ## Expected Behavior Pausing really pauses, not crashes. ## Reproduction *A minimal example that exhibits the behavior.* ```python from prefect import task, Flow, triggers @task def task_1(): return 1 @task(trigger=triggers.manual_only) def add_one(x): return x + 1 with Flow("example") as flow: t1 = task_1() t2 = add_one(x=t1) flow.run() # error ``` ## Environment *Any additional information about your environment* *Optionally run `prefect diagnostics` from the command line and paste the information here* 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: `c_if` fails when using indexing if there are no classical registers in the circuit <!-- ⚠ 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**: main - **Python version**: any - **Operating system**: any ### What is the current behavior? All `c_if` statements immediately fail if there are no classical registers defined in the circuit, only loose bits, and one tries to specify the condition with an index. ### Steps to reproduce the problem ```python In [1]: from qiskit.circuit import QuantumCircuit, Clbit, Qubit ...: ...: qc = QuantumCircuit([Qubit(), Clbit()]) ...: qc.x(0).c_if(0, 0) --------------------------------------------------------------------------- UnboundLocalError Traceback (most recent call last) <ipython-input-1-efd3b9b41798> in <module> 2 3 qc = QuantumCircuit([Qubit(), Clbit()]) ----> 4 qc.x(0).c_if(0, 0) ~/code/qiskit/terra/qiskit/circuit/instructionset.py in c_if(self, classical, val) 65 if isinstance(classical, (Clbit, int)): 66 if isinstance(classical, int): ---> 67 classical = circuit_clbits[classical] 68 for creg in self.circuit_cregs: 69 if creg[:] == [classical]: UnboundLocalError: local variable 'circuit_clbits' referenced before assignment ``` ### What is the expected behavior? There should be no error, and it should select the correct bit as a condition. ### Suggested solutions A similar fix to #7246 will work here as well. Can you help me debug this systematically and explain your reasoning?


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

[User]
I'm having an issue with the ipython/ipython codebase. Here's the problem: cannot export to notebook with magic command in IPython 3.0.0 I was trying to export command history into a notebook with `%notebook -e $notebook_file`, and got the following error:
/Users/w/python-venv/2.7/lib/python2.7/site-packages/IPython/core/magics/basic.pyc in notebook(self, s) 605 cells.append(v4.new_code_cell( 606 execution_count=execution_count, --> 607 source=source 608 )) 609 nb = v4.new_notebook(cells=cells) NameError: global name 'source' is not defined
 Had a quick look in the file `IPython/core/magics/basic.py`, and I guess the line `source=source` should be replaced by `source=input`? Here is the output of `python -c "import IPython; print(IPython.sys_info())"` on my system:
{'commit_hash': u'f75fda4', 'commit_source': 'installation', 'default_encoding': 'UTF-8', 'ipython_path': '/Users/w/python-venv/2.7/lib/python2.7/site-packages/IPython', 'ipython_version': '3.0.0', 'os_name': 'posix', 'platform': 'Darwin-14.1.0-x86_64-i386-64bit', 'sys_executable': '/Users/w/python-venv/2.7/bin/python', 'sys_platform': 'darwin', 'sys_version': '2.7.6 (default, Sep 9 2014, 15:04:36) \n[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)]'}
 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the explosion/spaCy codebase. Here's the problem: 💫 Lemmatizer should apply rules on OOV words @juanmirocks points out in #327 that the lemmatizer fails on OOV words: ```python >>> nlp.vocab.morphology.lemmatizer(u'endosomes', 'noun', morphology={'number': 'plur'})set([u'endosomes']) >>> nlp.vocab.morphology.lemmatizer(u'chromosomes', 'noun', morphology={'number': 'plur'}) set([u'chromosome']) ``` Suggested patch to lemmatizer.py ```python oov_forms = [] for old, new in rules: if string.endswith(old): form = string[:len(string) - len(old)] + new if form in index or not form.isalpha(): forms.append(form) else: oov_forms.append(form) if not forms: forms.extend(oov_forms) ``` ## Your Environment <!-- Include details of your environment --> * Operating System: * Python Version Used: * spaCy Version Used: * Environment Information: 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: Bizarre removal of python Full report at https://ci.appveyor.com/project/ContinuumAnalytics/conda-build/build/1.0.163#L18 ``` Package plan for installation in environment C:\Miniconda3-x64: The following packages will be downloaded: package | build ---------------------------|----------------- git-2.6.4 | 0 61.2 MB colorama-0.3.7 | py34_0 20 KB coverage-4.1 | py34_0 235 KB py-1.4.31 | py34_0 127 KB pytz-2016.4 | py34_0 171 KB six-1.10.0 | py34_0 17 KB clyent-1.2.2 | py34_0 15 KB pytest-2.9.2 | py34_0 283 KB python-dateutil-2.5.3 | py34_0 238 KB anaconda-client-1.4.0 | py34_0 156 KB pytest-cov-2.2.1 | py34_0 17 KB ------------------------------------------------------------ Total: 62.5 MB The following NEW packages will be INSTALLED: anaconda-client: 1.4.0-py34_0 clyent: 1.2.2-py34_0 colorama: 0.3.7-py34_0 coverage: 4.1-py34_0 git: 2.6.4-0 py: 1.4.31-py34_0 pytest: 2.9.2-py34_0 pytest-cov: 2.2.1-py34_0 python-dateutil: 2.5.3-py34_0 pytz: 2016.4-py34_0 six: 1.10.0-py34_0 The following packages will be REMOVED: python: 3.4.4-4 ``` CC @mcg1969 @kalefranz 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: Use apitools for uploads/downloads [`uploads_test.py`](https://github.com/craigcitro/apitools/blob/master/samples/storage_sample/uploads_test.py) and [`downloads_test.py`](https://github.com/craigcitro/apitools/blob/master/samples/storage_sample/downloads_test.py) should provide good examples for 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 google/jax codebase. Here's the problem: Inconsistent convention for complex derivatives The convention for the handling of complex derivatives in JAX seems to be mixed. Consider the following two implementations of the abolute value function. ```py import jax.numpy as np from jax import grad def f(x): return np.abs(x) def g(x): return np.sqrt(np.real(x)**2 + np.imag(x)**2) df = grad(f) dg = grad(g) print('gradient by df: ',df(1.0+0.5j)) print('gradient by dg: ',dg(1.0+0.5j)) ``` The respective results differ by complex conjugation: ``` gradient by df: (0.8944272-0.4472136j) gradient by dg: (0.8944272+0.4472136j) ``` 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: Uploading List of Files to Google Cloud Storage **Description** In the [current implementation](https://airflow.apache.org/docs/stable/_api/airflow/contrib/operators/file_to_gcs/index.html) of `FileToGoogleCloudStorageOperator`, a single file is inputted to be uploaded to Google Cloud Storage bucket. I'd like to implement functionality to allow input of a list of files, directory path or perhaps even a wildcard string (`/path/to/*.csv` for example). **Related Issues** Not that I can tell from searching, but there is this [stackoverflow question](https://stackoverflow.com/questions/58945050/uploading-local-directory-to-gcs-using-airflow) that @kaxil answered. 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: pdb no longer works with airflow test command since 2.3.3 Converted back to issue as I've reproduced it and traced the issue back to https://github.com/apache/airflow/pull/24362 ### Discussed in https://github.com/apache/airflow/discussions/26352
 Originally posted by **GuruComposer** September 12, 2022 ### Apache Airflow version 2.3.4 ### What happened I used to be able to use ipdb to debug DAGs by running `airflow tasks test <dag_name> <dag_id>`, and hitting an ipdb breakpoint (ipdb.set_trace()). This no longer works. I get a strange type error: ``` File "/usr/local/lib/python3.9/bdb.py", line 88, in trace_dispatch return self.dispatch_line(frame) File "/usr/local/lib/python3.9/bdb.py", line 112, in dispatch_line self.user_line(frame) File "/usr/local/lib/python3.9/pdb.py", line 262, in user_line self.interaction(frame, None) File "/home/astro/.local/lib/python3.9/site-packages/IPython/core/debugger.py", line 336, in interaction OldPdb.interaction(self, frame, traceback) File "/usr/local/lib/python3.9/pdb.py", line 357, in interaction self._cmdloop() File "/usr/local/lib/python3.9/pdb.py", line 322, in _cmdloop self.cmdloop() File "/usr/local/lib/python3.9/cmd.py", line 126, in cmdloop line = input(self.prompt) TypeError: an integer is required (got type NoneType)``` ### What you think should happen instead I should get the ipdb shell. ### How to reproduce 1. Add ipdb breakpoint anywhere in airflow task. import ipdb; ipdb.set_trace() 2. Run that task: Run `airflow tasks test <dag_name> <dag_id>`, and ### Operating System Debian GNU/Linux ### Versions of Apache Airflow Providers 2.3.4 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: AttributeError: 'str' object has no attribute '_credentials' Hi, I'm trying the example code and it's failing with the following exception: ``` >>> c = error_reporting.Client(project='<my-project-str>') >>> try: ... raise NameError ... except Exception: ... c.report_exception() ... Traceback (most recent call last): File "<stdin>", line 2, in <module> NameError During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<stdin>", line 4, in <module> File "/opt/python/3.6.0/lib/python3.6/site-packages/google/cloud/error_reporting/client.py", line 348, in report_exception user=user) File "/opt/python/3.6.0/lib/python3.6/site-packages/google/cloud/error_reporting/client.py", line 277, in _send_error_report self.report_errors_api.report_error_event(error_report) File "/opt/python/3.6.0/lib/python3.6/site-packages/google/cloud/error_reporting/client.py", line 162, in report_errors_api self._report_errors_api = make_report_error_api(self._project) File "/opt/python/3.6.0/lib/python3.6/site-packages/google/cloud/error_reporting/_gax.py", line 39, in make_report_error_api client._credentials, AttributeError: 'str' object has no attribute '_credentials' ``` Reading the source, this seems like a rather obvious error: https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/error_reporting/google/cloud/error_reporting/client.py#L162 `self._project` is a string and at https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/error_reporting/google/cloud/error_reporting/_gax.py#L29 it's treated like a client object. Is this not the case? Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Make ``VQE`` stateless ### Summary Make the `VQE` algorithm stateless. ### What is the expected enhancement All our algorithms are stateless, i.e. they don't store/depend on previous executions. The `VQE` still has methods that allow access to the last solved system, which should be strictly left to the results object. Furthermore the computation depends on an internal state being set, which should be changed to a procedural, stateless workflow. 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: GCloudErrors (like NotFound) should show the URL that was referenced Saying "the requested entity was not found" is useful if you're working with one entity only... otherwise it's just sort of like saying "something went wrong". If we're able to figure out the URL that raised the error, we should include it in the exception (and the `__str__` version of the exception. 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: [bug] missing CMakeUserPresets.json Conan 1.48.0 does not generate `CMakeUserPresets.json` if `conanfile.txt` used instead of `.py`. Probably this is duplicate of #11172. ### Environment Details * Operating System: linux * Conan version: 1.48.0 ### Steps to reproduce ``` cd "$(mktemp -d)" conan new hello/0.1 -m=cmake_exe rm conanfile.py echo -e "[generators]\nCMakeToolchain" > conanfile.txt mkdir build (cd build && conan install ..) tree "$(pwd)" ``` ### Output ``` /tmp/tmp.6FdEpSMGTR ├── CMakeLists.txt ├── build │ ├── CMakePresets.json │ ├── conan.lock │ ├── conan_toolchain.cmake │ ├── conanbuildinfo.txt │ ├── conaninfo.txt │ └── graph_info.json ├── conanfile.txt ├── include │ └── hello.h ├── src │ ├── hello.cpp │ └── main.cpp └── test_package └── conanfile.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 apache/airflow codebase. Here's the problem: BackfillJob eventually fails tasks when dependencies aren't met See https://github.com/airbnb/airflow/issues/1225#issuecomment-203153213 When dependencies are unmet, the command exists successfully (as in, without error or return code). The executor marks it as a success. But the task has no status, because it never ran. This triggers the "airflow run command failed to report an error" which eventually fails the task. This issue will be fixed as part of the resolution for #1225, this issue is for tracking 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 huggingface/transformers codebase. Here's the problem: MPT ### Model description New LLM from MosaicML, 7B parameters. See: https://www.mosaicml.com/blog/mpt-7b ### Open source status - [X] The model implementation is available - [X] The model weights are available ### Provide useful links for the implementation https://huggingface.co/mosaicml/mpt-7b/tree/main The model is already implemented in a HF/T compatible way, but has multiple source files for its model implementation, some components that aren't used in this current model, and most importantly, dependencies that aren't normally included in HF (e.g. einops, flash_attn). Do the HF folks have a view on whether we would want to add those dependencies, or implement a vanilla version based only on existing requirements (in which case, it would arguably be easier to modify an existing LM implementation instead, rather than use MosaicML's implemenetation)? 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: [bug] git clone for scm attribute fails in pyinstaller package Conan version 1.20.4 Original problem is that conan wrapped into pyinstaller package (which we use) fails to clone repository for recipe with `scm` attribute: ``` <...>: Configuring sources in /root/.conan/data/.../source <..>: Getting sources from url: 'ssh://git@bitbucket....' ERROR: Command 'git clone "ssh://git@bitbucket..." . ' returned non-zero exit status 128. ``` strace'ing showed that git fails to run because it uses libcrypto from conan (which is ancient) and can't find symbol. Apparently, conan doesn't restore `LD_LIBRARY_PATH` for `git clone` command. Similar problem was fixed long ago in #3036, but looking at `scm.py` / `run()` it has optional `_runner` which calls just `check_output` without restoring. If having `_runner` all the time is not an option, at least call to `check_output` should be wrapped into `pyinstaller_bundle_env_cleaned()` context manager. It would be nice to go through all calls to `Popen` and check whether they need to be wrapped into this context manager or maybe avoid direct usage of it and have an internal wrapper. 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: Alter signature of Client.set_flow_run_state ## Current behavior *Please describe how the feature works today* Currently, the `Client.set_flow_run_state(flow_run_id, state)` call always returns `None`. Unlike the task equivalent, which returns the new `State` object. All places where the client is calling this method are implicitly handling the state change by creating the new state, calling the method, then proceeding with that new state. ## Proposed behavior *Please describe your proposed change to the current behavior* The `set_flow_run_state` call should return the new `State` for a couple reasons. First, and most importantly, in order to extend the `Flow`'s options of states (instead of Pending -> Running -> Success / Failed), we need to be able to implement logic of listening to Cloud's response to the state change event. Secondly and less important, returning the new `State` for both the task and flow client calls would be nice for consistency reasons. ## Example *Please give an example of how the enhancement would be useful* While this feature itself won't change the current behavior, it will allow extension of Flow state control in the future! 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: Incorrect link in documentation There is an incorrect link at https://googlecloudplatform.github.io/google-cloud-python/latest/bigquery/dataset.html#google.cloud.bigquery.dataset.Dataset.delete. It links to https://cloud.google.com/bigquery/docs/reference/rest/v2/tables/delete, but it should link to https://cloud.google.com/bigquery/docs/reference/rest/v2/datasets/delete. Can you help me debug this systematically and explain your reasoning?