[System] You are an expert software 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: BackendConfiguration fails validation if backend supports pulse <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Informations - **Qiskit Terra version**:0.8.0 - **Python version**3.6.6 - **Operating system**:OSX ### What is the current behavior? If a backend sets `open_pulse=true` in its configuration Qiskit will raise a validation error when creating a `BackendConfigurationSchema` ### Steps to reproduce the problem Create a backend with `open_pulse=true` set in its configuration. ### What is the expected behavior? Should not fail. ### Suggested solutions Allow `open_pulse=true` to be valid. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Convert 12-1 and 6-1 en-de models from AllenNLP https://github.com/jungokasai/deep-shallow#download-trained-deep-shallow-models + These should be FSMT models, so can be part of #6940 or done after. + They should be uploaded to the AllenNLP namespace. If stas takes this, they can start in stas/ and I will move them. + model card(s) should link to the original repo and paper. + I hope same en-de tokenizer already ported. + Would be interesting to compare BLEU to the initial models in that PR. There is no ensemble so we should be able to reported scores pretty well. + **Ideally** this requires 0 lines of checked in python code, besides maybe an integration test. Desired Signature: ```python model = FSMT.from_pretrained('allen_nlp/en-de-12-1') ``` Weights can be downloaded with gdown https://pypi.org/project/gdown/ ```bash pip install gdown gdown https://drive.google.com/uc?id=1x_G2cjvM1nW5hjAB8-vWxRqtQTlmIaQU ``` @stas00 if you are blocked in the late stages of #6940 and have extra cycles, you could give this a whirl. We could also wait for that to be finalized and then either of us can take 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: pyreadline version dependency not correctly checked Installing IPython on windows with `python setup.py install` and pyreadline 1.5: <pre> C:\code\dev_trees\ipython [main-master]> ipython Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] Type "copyright", "credits" or "license" for more information. IPython 0.13.dev -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. Traceback (most recent call last): File "C:\Python26\Scripts\ipython-script.py", line 9, in <module> load_entry_point('ipython==0.13.dev', 'console_scripts', 'ipython')() File "C:\Python26\lib\site-packages\ipython-0.13.dev-py2.6.egg\IPython\frontend\terminal\ipapp.py", line 409, in launch_new_instance app.start() File "C:\Python26\lib\site-packages\ipython-0.13.dev-py2.6.egg\IPython\frontend\terminal\ipapp.py", line 383, in start self.shell.mainloop() File "C:\Python26\lib\site-packages\ipython-0.13.dev-py2.6.egg\IPython\frontend\terminal\interactiveshell.py", line 290, in mainloop self.interact(display_banner=display_banner) File "C:\Python26\lib\site-packages\ipython-0.13.dev-py2.6.egg\IPython\frontend\terminal\interactiveshell.py", line 346, in interact hlen_b4_cell = self.readline.get_current_history_length() AttributeError: 'module' object has no attribute 'get_current_history_length' </pre> I see that `setup.py` `requires` pyreadline >= 1.7.1, iff `setupext.check_for_readline()` returns False. However, in my case, it returns True because the function does not check the version, and I have version 1.5. I wasn't sure how best to put the version dependency into the function. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Invalid XML generated in testlog.junit.xml with \x07 in test output **Describe the bug** I was running tests with meson and the output of one of my tests contains special character `\x07`. When I run testlog.junit.xml through xmllint, I get an error saying: `testlog.junit.xml:11045: parser error : PCDATA invalid Char value 7` I think we should use the right escape characters so that the output is valid XML. **To Reproduce** I wrote a simple meson.build file to reproduce this issue. The code in the file is: ``` project('tutorial', 'c') test('mytest',find_program('python'), args: ['-c','print(u"Test\x07")']) ``` I then ran `meson setup`, followed by `ninja test` to run it and generate the `testlog.junit.xml` file. Then, running: `xmllint builddir/meson-logs/testlog.junit.xml` outputs an error message: ``` builddir/meson-logs/testlog.junit.xml:2: parser error : PCDATA invalid Char value 7 e name="mytest" classname="tutorial" time="0.06694579124450684"><system-out>Test ``` **Expected behavior** I think the character should be correctly escaped so that the output is valid XML. **system parameters** OS: MacOS Monterey (12.1) meson --version 0.61.1 ninja --version 1.10.2 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 ipython/ipython codebase. Here's the problem: can't configure inline plot in qtconsole This problem exists in ipython 3.0.dev (git master), but not in ipython 2.1. Has the configuration system changed in 3.0? Suppose I have the following lines in my ~/.ipython/profile_default/ipython_qtconsole_config.py ``` python c.IPythonWidget.font_size = 20 c.InlineBackend.rc = {'font.size': 18, 'figure.figsize': (9.0, 6.0)} ``` If I start ipython by $ ipython qtconsole --pylab=inline then IPythonWidget.font_size is correctly handled but InlineBackend.rc is ignored. ipython 3.0 (git master) matplotlib 1.5 (git master) MacOSX 10.8.5 / Python 2.7.2 (Apple) Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Feature request: IFFT Hi there! I'm finding Jax to be very useful in my work, but a new project (spectral Gaussian process stuff) requires me to differentiate through both FFT and IFFT operations. It is possible to express IFFT in terms of FFT, but it would be cleaner to just have an IFFT primitive, I think. Thank you! edit: also, vmap support would be very helpful as well. Also for people from the future, here is an implementation using FFT only: ```python from typing import Optional, Sequence def ifftn( a: np.ndarray, s: Sequence[int] = None, axes: Sequence[int] = None, norm: Optional[str] = None, ) -> np.ndarray: """Compute the n-dimensional inverse Fourier transform. Args: a: Input array. s: Shape of the output. axes: Axes over which to compute the IFFT. norm: Normalization mode, one of ``None`` or ``"ortho"``. Returns: The n-dimensional IFFT of ``a``. """ if s is not None: raise NotImplementedError if norm is not None: raise NotImplementedError n = np.prod(np.array(a.shape)[axes]) return (1 / n) * np.conj(np.fft.fftn(np.conj(a), axes=axes)) ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: %cpaste doc error: Magics ARE supported `%cpaste?` claims "IPython statements (magics, shell escapes) are not supported (yet)." But at least magics apparently are! Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: PauliExpectation warning given unexpectedly When running the following test https://github.com/Qiskit/qiskit-nature/blob/01ec334a18fbcf2368765dfd2d522e116da9de0e/test/algorithms/ground_state_solvers/test_groundstate_eigensolver.py#L334 it prints this message unexpectedly to me. `Measured Observable is not composed of only Paulis, converting to Pauli representation, which can be expensive.` In looking it seems to be when the expectation is taken of the aux_operators. This is a ListOp of PauliSumOps i.e. a List of a number of different operators like dipole X, num particles etc of which an expectation is computed against the result state of VQE to measure these. Now at the time of writing this test is failing to meet the final result. That's a different problem than the above but in looking at that is when I saw this message appearing Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: 0.8.2 calls backward on '_GeneratorContextManager' ## 🐛 Bug 0.8.2 calls backward on '_GeneratorContextManager' and crashes training. 0.8.1 works correctly. my `training_step` returns `{'loss':loss, 'log':{'learn_rate':self.lr}}` ``` Traceback (most recent call last): File "/opt/conda/lib/python3.6/site-packages/torch/multiprocessing/spawn.py", line 20, in _wrap fn(i, *args) File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/distrib_data_parallel.py", line 538, in ddp_train self.run_pretrain_routine(model) File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/trainer.py", line 1100, in run_pretrain_routine self.train() File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/training_loop.py", line 370, in train self.run_training_epoch() File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/training_loop.py", line 452, in run_training_epoch batch_output = self.run_training_batch(batch, batch_idx) File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/training_loop.py", line 630, in run_training_batch self.hiddens File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/trainer/training_loop.py", line 804, in optimizer_closure model_ref.backward(self, closure_loss, optimizer, opt_idx) File "/opt/conda/lib/python3.6/site-packages/pytorch_lightning/core/hooks.py", line 189, in backward loss.backward() AttributeError: '_GeneratorContextManager' object has no attribute 'backward' ``` ### Expected behavior backward is called on the loss and training runs correctly Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: document lax.axis_index to get mapped element index from axis name Hello JAX team, First of all, thanks a lot for cool JAX. This is a great tool. This issue contains a question about your plans regarding `pmap` and a feature request. What `pmap`ed function receives as an input, is that a slice of input array or a full array? What happens in case of nested `pmap`s? Guess JAX traces a function and runs copies of it on sharded chunks of an input array. If so, that would super useful to have access to an index of that shard, that would allow encoding more complex algorithms. Otherwise, it still would be great to have an access to the shard index. <details><summary>Example</summary> <p> ```python @partial(pmap, axis_name='rows') @partial(pmap, axis_name='cols') def f(x): # Q: When the code is running, what the `x.shape` actually is? # # Dummy example of how to get shard id: # shard_row_id = __global_axis_name__["rows"] # shard_col_id = __global_axis_name__["cols"] # # Do something smart with it! E.g. process tensor in `chess` like style - blacks are positive, whites are negative. pass ``` </p> </details> Thanks Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Difference between `logit_scale` initialisation in Transformers CLIP and the original OpenAI implementation. I tried another training code based on the OpenAI'CLIP version: I found a difference at logit_scale between them. Does it mean temperature parameter? Is it the reason for loss rising? huggingface transformers' CLIP: ``` self.logit_scale = nn.Parameter(torch.ones([])) ``` OpenAI CLIP: ``` self.logit_scale = nn.Parameter(torch.ones([]) * np.log(1 / 0.07)) ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: fetch_data() should return a core iterator See: [https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/bigquery/google/cloud/bigquery/query.py#L363][1] ```python def fetch_data(...): """... :returns: ``(row_data, total_rows, page_token)`` ... """ ``` I would expect it to return some kind of [Iterator](https://github.com/GoogleCloudPlatform/google-cloud-python/blob/master/core/google/cloud/iterator.py) to be consistent with the other cloud APIs. [1]: https://github.com/GoogleCloudPlatform/google-cloud-python/blob/2d9c109211331c6cfc59a2a9acbda4c4e3609509/bigquery/google/cloud/bigquery/query.py#L363 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the docker/compose codebase. Here's the problem: Support ulimit options Now that Docker 1.6 supports ulimit options, it would be nice to have this as an option for containers managed by compose, similar to `mem_limit`, `cpu_shares`, 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 mesonbuild/meson codebase. Here's the problem: Should meson specifiy -release for DLang projects with the `plain` buildtype? Right now meson doesn't specify `-release` on the compiler command line when compiling with the `plain` buildtype. This is problematic, since the `-release` flag doesn't do unwanted optimizations distros want to avoid, it disables asserts, quoting the LDC docs: `-release | Disables asserts, invariants, contracts and boundscheck` [0]. Since distros usually use the `plain` buildtype, but don't want debug asserts, contracts (input validation for functions, also via asserts) etc. in their binaries it'd make sense to specify `-release` even with the `plain` buildtype IMHO. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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] [develop2] Order new hook_ hooks Alphabetically, so at least there is an order defined for all hooks found in the cache. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the docker/compose codebase. Here's the problem: docker-compose $(docker-machine config default) up Fails. docker and docker-compose handle arguments differently. `docker-compose $(docker-machine config default) up`causes an error. (see below) and `docker-compose $(docker-machine config default | xargs) up` works. joe@jsd-mbp ~ $ docker-compose $(docker-machine config default) -f docker-compose.yml up [2.2.3] Traceback (most recent call last): File "<string>", line 3, in <module> File "compose/cli/main.py", line 58, in main File "compose/cli/main.py", line 106, in perform_command File "compose/cli/command.py", line 33, in project_from_options File "compose/cli/docker_client.py", line 36, in tls_config_from_options File "site-packages/docker/tls.py", line 47, in **init** docker.errors.TLSParameterError: Path to a certificate and key files must be provided through the client_config param. TLS configurations should map the Docker CLI client configurations. See https://docs.docker.com/engine/articles/https/ for API details. docker-compose returned -1 joe@jsd-mbp ~ $ Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Regression in conda 4.3.33 regarding build features It seems that `conda 4.3.33` installs packages that have a build feature when installing any package that has the same build feature. From a fresh miniconda, with conda pinned at `4.3.32`: ```sh scorlay@mbp ~]$ conda install cryptopp -c QuantStack -c conda-forge Fetching package metadata ............... Solving package specifications: . Package plan for installation in environment /Users/scorlay/miniconda3: The following NEW packages will be INSTALLED: cling-patches: 1-0 QuantStack cryptopp: 5.6.5-cling_0 QuantStack [cling] ``` With `conda 4.3.33` ```sh [scorlay@mbp ~]$ conda install cryptopp -c QuantStack -c conda-forge Fetching package metadata ............... Solving package specifications: . Package plan for installation in environment /Users/scorlay/miniconda3: The following NEW packages will be INSTALLED: clangdev: 5.0.0-cling_1 QuantStack [cling] cling-patches: 1-0 QuantStack cryptopp: 5.6.5-cling_0 QuantStack [cling] icu: 58.2-0 conda-forge libiconv: 1.15-0 conda-forge libxml2: 2.9.7-0 conda-forge llvmdev: 5.0.0-cling_1 QuantStack [cling] ``` The only package tracking the `cling` build feature is `cling-patches`. Notice in the second case that `clangdev` gets installed while it is not a dependency. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Sqrt(X) and C-Sqrt(X) gates We should add these two gates. The first one is the current native hardware gate that is tuned up (a.k.a X90p or RX(pi/2) although I think there's a global phase difference). The second one gives more efficient oracles via better Toffolis. Let's call them SX and CSX for now (although V and CV also appear in the literature). Then we should try to replace all usages of U2 with the SX gate (conjugated by RZ), which would put us on a path towards https://github.com/Qiskit/qiskit-terra/issues/4106. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Tensorboard logging in multi-gpu setting not working properly? Hi there :) I have a question (that may be an issue with the code or just my ignorance). (b.t.w. I am using the latest version, pytorch-lightning==0.4.9) If I set the trainer `trainer = Trainer(experiment=exp, gpus=[0])` I can see the corresponding logging (scalars and hyperparameters) in Tensorboard. If I change it to distributed training (keeping the rest of the code unchanged) : ` trainer = Trainer(experiment=exp, gpus=[0,1], distributed_backend='ddp')` The Tensorboard logging stops working at least for scalars and hyperparameters, I see nothing except the experiment name. In both cases 'exp' is a Experiment instantiated like this: ` exp = Experiment(save_dir=/SOME/PATH, name=NAME, version=VERSION, description=DESCRIPTION)` This picture illustrates the problem. ![Untitled](https://user-images.githubusercontent.com/2588285/65029817-b175d500-d93e-11e9-9f3f-3e350d4188d4.png) In the picture the red arrows point to the "distributed" experiment, with no drawing in the chart. The other two (the ones that appear in the chart) are the very same, except than the run in single GPU. Am I missing something or do I need to add extra configuration to make the logging work in multi-gpu with the ddp setting? Or is it a bug? Thank you! :) Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: i18n: allow to use keywords in i18n.merge_file() It needed for libpeas-based plugin systems and another plugin systems, which relies on keyfile-based configs. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Extra blank line needed in multi-line Thanks for the all the fast fixes so far. This is really minor, so feel free to punt, but it has been tripping me up a little. In 5.0, if a function contains a return statement, it takes 1 extra line to close the multi-line block compared to previous behavior. Note that if that function (or more realistically, an `if` block) doesn't end in a `return`/`pass`, then the old behavior persists. Let me know if these examples aren't clear. #### 4.x ``` In [3]: def f(a): ...: return 5 ...: ``` #### 5.0b2 ``` In [10]: def f(a): ...: return 4 ...: ...: In [11]: def f(a): ...: a = 5 ...: ``` Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Create UndefinedJinjaVariablesRule to ease upgrade to 2.0 This issue is part of #8765 ## Rule Create `UndefinedJinjaVariablesRule` which corresponds to > Prior to Airflow 2.0 Jinja Templates would permit the use of undefined variables. They would render as an empty string, with no indication to the user an undefined variable was used. With this release, any template rendering involving undefined variables will fail the task, as well as displaying an error in the UI when rendering. entry in UPDATING.md. Introduced in #11016 This rule should check if any of the jinja templates use undefined variables. This might not be always possible, as this might involve the dynamic generation of some context variables, but likely we can at least print some warning or "double-check this" statements. ## How to guide To implement a new rule, create a class that inherits from `airflow.upgrade.rules.base_rule.BaseRule`. It will be auto-registered and used by `airflow upgrade-check` command. The custom rule class has to have `title`, `description` properties and should implement `check` method which returns a list of error messages in case of incompatibility. For example: https://github.com/apache/airflow/blob/ea36166961ca35fc51ddc262ec245590c3e236fb/airflow/upgrade/rules/conn_type_is_not_nullable.py#L25-L42 **Remember** to open the PR against `v1-10-test` branch. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: HfArgumentParser doesn't recognize new list type hint syntax Since Python 3.9 we can use generic types as type hints (e.g. `list[str]` instead of `typing.List[str]`), see also [PEP 585](https://www.python.org/dev/peps/pep-0585/). Currently this does not seem to work with the `HfArgumentParser`, but using the old `typing.List[str]` works. Minimal example for an arguments data class: ```python @dataclass class Args: my_boring_argument_list: typing.List[str] # works my_cool_argument_list: list[str] # fails ``` Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Allow for different "Spins" We should allow for pre-built applications to be distributed that do not depend on the JupyterLab Python package (and its server extension). All that is needed to accommodate this is a separate Python package that exposes a function that takes a notebook app, a config directory and a prefix and adds the appropriate handlers. The package will also include an `index.html` template. An application author would use the main JupyterLab package to build its assets, and the app launcher to launch the application. The main JupyterLab package will use the app launcher in its server extension, and also include its built assets. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Cleanup duplicated "credentials can not sign" error Context: https://github.com/GoogleCloudPlatform/google-cloud-python/pull/2998#discussion_r100650121 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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` to `DAGCircuit.substitute_node_with_dag` Similar to `DAGCircuit.compose`, we need to ensure that the mapping of conditions and targets works with the general `Expr` format of classical values. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Boolean function parser We need a way to express Boolean functions compactly (e.g. f(x1,x2) = x1^x2), without resorting to exponential descriptions. Right now we only do things like truth table descriptions using exponential arrays (in synthesis algorithms like graysynth and libraries like FourierChecking). Some tools for this exist as opensource like RevKit and the Tweedledum library. Then we can also have synthesis algorithms for these that do not rely on synthesis of diagonal operators, and use those for synthesizing FourierChecking, Forrelation, HiddenShift, etc. 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 conan-io/conan codebase. Here's the problem: [feature] Create "new --template" for Autotools. Like https://github.com/conan-io/conan/pull/10760/files but for Autotools. Tests using it, even with windows subsystems. Better study if a predefined layout is convenient. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: BQML `get_model` snippets tests are failing https://github.com/googleapis/google-cloud-python/pull/8049#issuecomment-494463181 Appears that there's a new field in the response message. I thought protobuf was supposed to ignore unknown fields, but maybe that's not the default. I'll see if I can get a fix today to the Python client. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Lightning-AI/lightning codebase. Here's the problem: "limit_train_batches" not receiving float value <!-- ### Common bugs: 1. Tensorboard not showing in Jupyter-notebook see [issue 79](https://github.com/PyTorchLightning/pytorch-lightning/issues/79). 2. PyTorch 1.1.0 vs 1.2.0 support [see FAQ](https://github.com/PyTorchLightning/pytorch-lightning#faq) --> ## 🐛 Bug error: argument --limit_train_batches: invalid int value: '0.3' ### To Reproduce Just put any float value after '--limit_train_batches' or '--val_check_interval' I am using the latest master branch. 0.9.rc14 I think this issue is related to the fix of #2943 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: CmdDef from_defaults does not add buffer to channels. <!-- ⚠ 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? Command definition is built with a buffer of 0 for channels. ### Steps to reproduce the problem ### What is the expected behavior? ### Suggested solutions Add the defaults buffer to the channels when building the CmdDef. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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] Make ConanApiAuthManager and RestClient concurrent https://github.com/conan-io/conan/pull/5856 is failing. The problem is that the auth-restclient layer is not designed for concurrency, and it has a single instance of user, remote, remote.url, and auth-tokens for all the calls. It is necessary to implement this feature to unblock the concurrent uploads. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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 valac.find_library Vala library (`.vapi`) names don't always match the pkg-config name, and sometimes the C library doesn't even have a pkg-config file so we need a `valac.find_library()` to be able to find those. Related to #687. I'm planning on working on this, and I think we should get this in for 0.36, so I thought I'd file an issue for it too. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: [Examples][Flax] AttributeError: 'DataTrainingArguments' object has no attribute 'test_file' ## Description While running run_summarization_flax.py with local files, currently we have only two DataTrainingArguments, one for training and another for validation file still we are validating test_file which is producing an error ``` Traceback (most recent call last): File "transformers/examples/flax/summarization/run_summarization_flax.py", line 808, in <module> main() File "transformers/examples/flax/summarization/run_summarization_flax.py", line 352, in main if data_args.test_file is not None: AttributeError: 'DataTrainingArguments' object has no attribute 'test_file' ``` ## Environment info - `transformers` version: 4.9.0(master branch) - Platform: TPU VM - Python version: 3.9 - PyTorch version (GPU?): - Tensorflow version (GPU?): - Using GPU in script?: - Using distributed or parallel set-up in script?: ### Who can help @sgugger, @patil-suraj ### Possible Fix: Either we can add test_file argument or remove test file validation section https://github.com/huggingface/transformers/blob/7d6285a921a23c06169e2d90c94faa0d92d00d78/examples/flax/summarization/run_summarization_flax.py#L352-L354 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Add git hooks for updating js @fperez suggested adding a directory of git hooks like in the notebook (https://github.com/jupyter/notebook/tree/master/git-hooks) so that pulling or merging will automatically rebuild the js and update the server extension. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: add 'QueryJob.estimates_bytes_processed' property See [API ref](https://cloud.google.com/bigquery/docs/reference/rest/v2/jobs#statistics.query.estimatedBytesProcessed). Read-only, based on the `statistics.query.estimatedBytesProcessed` field. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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? hstack/vstack/column_stack no longer accept generators As reported by @ilayn over in https://github.com/numpy/numpy/issues/12262: > There are other backwards incompatible changes for hstack and column_stack which were explicitly accepting generator expressions but now they don't. > > Xref : scipy/scipy#9405 Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: mpl drawer: unitary gate looks messy for 1 qubit <!-- ⚠ 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? If I add unitary gates to the circuit, they show up fine in the `mpl` drawer except for the 1-qubit case. The single-qubit case should also not print the full matrix, and just do a box labeled "unitary". ```python from qiskit import QuantumRegister, QuantumCircuit from qiskit.quantum_info.random import random_unitary qr = QuantumRegister(4) qc = QuantumCircuit(qr) U1 = random_unitary(2) U2 = random_unitary(4) U3 = random_unitary(8) U4 = random_unitary(16) qc.append(U1, [qr[0]]) qc.append(U2, [qr[0], qr[1]]) qc.append(U3, [qr[0], qr[1], qr[2]]) qc.append(U4, [qr[0], qr[1], qr[2], qr[3]]) qc.draw(output='mpl') ``` ![image](https://user-images.githubusercontent.com/8622381/56902007-64fd2c00-6a67-11e9-81f5-79c985cb4dab.png) Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: cross compilation doesn't support the "--strip" option cross_file.txt: c = '/opt/br_mips-2013.11/usr/bin/mips-linux-gcc' cpp = '/opt/br_mips-2013.11/usr/bin/mips-linux-g++' ar = '/opt/br_mips-2013.11/usr/bin/mips-linux-ar' strip = '/opt/br_mips-2013.11/usr/bin/mips-linux-strip' [host_machine] system = 'linux' cpu_family = 'mips' cpu = 'mips' endian = 'big' Without the "-strip" option it works fine: meson --cross-file ../../../../lte1160/cross_file.txt . $d --prefix=$HOME/tmp/meson ninja-build -C build ninja-build -C build install With the "-strip" option it doesn't work: meson --cross-file ../../../../lte1160/cross_file.txt . $d --prefix=$HOME/tmp/meson --strip ninja-build -C build ninja-build -C build install Stripping target 'libkt_dmc_cm-1.0.so' Could not strip file. Stdout: Stderr: strip: Unable to recognise the format of the input file `/home/fabiopo/tmp/meson/lib64/libkt_dmc_cm-1.0.so' FAILED: install '/usr/bin/python3' '/home/fabiopo/packages/meson/meson.py' '--internal' 'install' '/ssd/lte/app-2/tcommon/src/oma-dm/kt_lib/build/meson-private/install.dat' ninja: build stopped: subcommand failed. I'm doing something wrong? It is expected? Any suggestion on how to fix it? Thanks Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Fail to send class definitions from interactive session to engines namespaces Here is a [sample notebook](http://nbviewer.ipython.org/4471180/) to demonstrate the issue. Please note that I don't get any unpickling error message when calling: ``` rc[:]['AClass'] = AClass ``` While @minrk is reporting a `DummyModule` `AttributeError` in this [SO question](http://stackoverflow.com/questions/14184621/how-to-work-with-interactively-defined-classes-in-ipython-parallel). I will see if I can come up with a pull request for a `can_class` / `uncan_class` along the lines of [this gist](https://gist.github.com/4470212). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: How to pass include directories / CFlags to gtkdoc-scangobj ? I'm probably not understanding something here, but I need to pass additionnal flags to scangobj: * `include_directories` to specific dirs of the project * `link_with` helper/static libraries of the project It seems that the only way to do that is to `declare_dependency` with those infos and pass this dependency to `gnome.gtkdoc`. Isn't there an easier way ? EDIT: That doesn't work, because `meson.source_root()` is a relative path, and the scanobj call is equivalent to: cd devel-docs/libgimp && gtkdoc-scangobj --cflags=... --ldflags=... That seems to break the path to `meson.source_root() == ../.`. Or am i missing something ? Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [bug] CMakeToolchain always enables CMAKE_POSITION_INDEPENDENT_CODE ### Steps to reproduce (Include if Applicable) Using the CMakeToolchain generator, run `conan install` and disable `fPIC` option. The generated CMakeToolchain file will contain `CMAKE_POSITION_INDEPENDENT_CODE=ON`. This is obviously due to a typo fixed by #9752 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: up --force-recreate fails with tmpfs on volume you can reproduce this with thoses 2 files: ``` version: '2' services: test: build: . tmpfs: /mnt/tmpfs ``` ``` FROM alpine:3.4 VOLUME /mnt/tmpfs CMD /bin/sh ``` then run: * `docker-compose up -d` this one works * `docker-compose up -d --force-recreate` this one fails with this message: > Recreating tmp_test_1 ERROR: for test Cannot create container for service test: Duplicate mount point '/mnt/tmpfs' ERROR: Encountered errors while bringing up the project. version of Docker : Docker version 1.12.2, build bb80604 and tested with 2 versions of docker compose: * docker-compose version 1.8.0, build f3628c7 * docker-compose version 1.9.0-rc4, build 181a4e9 At first I thought it was the same issue as docker/docker#23301 but if this was still an issue the first `docker-compose up -d` should have failed too. So I'm not sure if this is a problem with docker-compose or with docker itself as I don't really know what docker-compose does on `--force-recreate` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: [hparams] save_hyperparameters doesn't save kwargs ## ❓ Questions and Help when I use hyperparemeters like docs: ``` class LitMNIST(LightningModule): def __init__(self, layer_1_dim=128, learning_rate=1e-2, **kwargs): super().__init__() # call this to save (layer_1_dim=128, learning_rate=1e-4) to the checkpoint self.save_hyperparameters() ``` model checkpoint doesn't save args in kwargs. But kwargs is important. Args such as `num_frames, img_size, img_std ...` must be used in creating `dataloader`, but it will be tedious if writes them in `__init__` explicitly . it can make code clean if hides them in `kwargs`. Before I use `hparams`, it's ok. But now it's not recommended to use `hparams`, is there any good idea to deal with this problem? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: cmake_find_package_generator does not generate guards To help us debug your issue please explain: Ubuntu 16.04, conan 1.5.1, cmake 3.11.4: Using the cmake_find_package generator with a project that calls find_package multiple times on the same library is not safe because the generated find_package script does not guard against being called multiple times. Since the script generates targets, this will cause cmake to fail the build. - [x] I've read the [CONTRIBUTING guide](https://raw.githubusercontent.com/conan-io/conan/develop/.github/CONTRIBUTING.md). - [x] I've specified the Conan version, operating system version and any tool that can be relevant. - [x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: mesonconf and meson should accept same flags `meson` takes `--prefix=/foo` `mesonconf` takes `-Dprefix=/foo` It would be nice for these to be consistent for both users and tools and for unknown ones to error. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Task library: add Filter When working with mapped tasks, it's common to have one or more children tasks skip or fail (for any reason). Anticipating these non-success states can complicate users who want to reduce over the result of a map, because they need to set custom trigger settings on the reducing task as well as handle the non-success results (`NoResult` and `Exceptions`). A "Filter" task (open to any other name) would essentially be the following: ```python class Filter(Task): def __init__(self, **kwargs): super().__init__(trigger=all_finished, skip_on_upstream_skip=False, **kwargs) def run(self, mapped_result): return [r for r in mapped_result if not isinstance(r, (NoResult, Exception))] ``` And used like this: ```python numbers = [1, '2', 3] numbers_plus_one = plus_one.map(numbers) good_results = Filter()(numbers_plus_one) ``` good_results would return `[1, 3]` -- having filtered the map for only the useful tasks. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the mesonbuild/meson codebase. Here's the problem: MSVC build fails owing to overly long build directory names So I'm building `gst-build` on Windows, with glib as a subproject. The build fails with the following error message: `[1/1857] Compiling C object subprojects/glib/gio/tests/gdbus-object-manager-example/subprojects@glib@gio@tests@gdbus-object-manager-example@@libgdbus-example-objectmanager@sha/meson-generated_.._gdbus-example-objectmanager-generated.c.obj. FAILED: subprojects/glib/gio/tests/gdbus-object-manager-example/subprojects@glib@gio@tests@gdbus-object-manager-example@@libgdbus-example-objectmanager@sha/meson-generated_.._gdbus-example-objectmanager-generated.c.obj cl @subprojects/glib/gio/tests/gdbus-object-manager-example/subprojects@glib@gio@tests@gdbus-object-manager-example@@libgdbus-example-objectmanager@sha/meson-generated_.._gdbus-example-objectmanager-generated.c.obj.rsp subprojects/glib/gio/tests/gdbus-object-manager-example/gdbus-example-objectmanager-generated.c: fatal error C1041: cannot open program database 'subprojects\\glib\\gio\\tests\\gdbus-object-manager-example\\subprojects@glib@gio@tests@gdbus-object-manager-example@@libgdbus-example-objectmanager@sha\\meson-generated_.._gdbus-example-objectmanager-generated.c.pdb'; if multiple CL.EXE write to the same .PDB file, please use /FS ` Turns out the problem is the overly long build directory paths here, exceeding the default 260 path limit. The build works fine if I use `c:\build` as build directory instead. I understand why these paths might be needed in the flat layout case, but Meson knows that we don't use a flat layout here, so I think it shouldn't be using these long cluttery paths in this 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 PrefectHQ/prefect codebase. Here's the problem: Add a few `flow.visualize()` unit tests We should have a few tests just to make sure the colors work, etc. Adding this as a small, low priority issue for picking up whenever any of us need some added diversity of tasks Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: Convert `BIPMaping` transpiler pass into an external plugin ### What should we add? The [`BIPMapping` transpiler pass](https://qiskit.org/documentation/stubs/qiskit.transpiler.passes.BIPMapping.html) has been in a weird state since it's introduction. It is a standalone transpiler pass that is used for both the layout and routing stage but we never integrated it into `transpile` because it has an external dependency on `cplex` which is a proprietary software package that most people don't have access too.. Now that we've added an external plugin interface for transpiler stages (which was added in #8305) we have a better option for how to advertise and use the `BipMapping` pass. We can create an external package for the pass that contains the code of the transpiler pass and offers a plugin that cleanly integrates into the `transpile()` function. Basically the workflow for using the bip mapper would change to be `pip install qiskit-bip-mapper` (or whatever the package name we pick is) and then doing `transpile(qc, backend, layout_method="bip_mapping")`. This make it easier for users to run and also separates the dependency on cplex into a separate package where we can more cleanly document the extra requirements around installing and/or purchasing a commercial license depending on the size of the circuits. Steps: - [x] Create a new package for the `BipMapping` pass - [x] Add layout plugin for the pass - [x] Deprecate `BIPMapping` pass in qiskit-terra after release of p Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: '_AsyncQuery.cancel' fails to update from returned resource E.g.: ``` python Traceback (most recent call last): File ... job.cancel() File ".../google/cloud/bigquery/job.py", line 378, in cancel self._set_properties(api_response) File ".../google/cloud/bigquery/job.py", line 262, in _set_properties self._scrub_local_properties(cleaned) File ".../google/cloud/bigquery/job.py", line 1050, in _scrub_local_properties configuration = cleaned['configuration']['query'] KeyError: 'configuration' ``` The [docs for `job.cancel`](https://cloud.google.com/bigquery/docs/reference/v2/jobs/cancel#response) show that the job resource is in a `job` subkey of the response. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the huggingface/transformers codebase. Here's the problem: Enable ONNX export for `VisionDecoderEncoderModel` # 🚀 Feature request <!-- A clear and concise description of the feature proposal. Please provide a link to the paper and code in case they exist. --> As discussed on the [forums](https://discuss.huggingface.co/t/can-i-export-a-visionencoderdecoder-checkpoint-to-onnx/12885), it would be nice if one could export `VisionDecoderEncoderModel` classes using the `transformers.onnx` package. ## Motivation <!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too. --> It is currently not possible to export `VisionDecoderEncoderModel` classes (or vision models more generally), unless the end user is willing to write their own `OnnxConfig`. It might make sense to first explore what is involved in exporting ViT before tackling this more complex example. Looking at this a bit more closely, I can see that `transformers.onnx` currently has a tight integration with tokenizers (e.g. to generate dummy inputs), so some refactoring will be necessary to support other modalities. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: text drawer bug in drawing conditional multi-qubit gates <!-- ⚠ 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? Conditional versions of 2-qubit or 3-qubit gates are drawn incorrectly in the text drawer. The box is drawn on only one of the qubits, whereas it should be 2 or 3 qubits. ```python qr = QuantumRegister(3, 'qr') cr = ClassicalRegister(2, 'cr') circuit = QuantumCircuit(qr, cr) circuit.cz(qr[0], qr[1]).c_if(cr, 1) circuit.ccx(qr[0], qr[1], qr[2]).c_if(cr, 3) ``` ``` ┌────┐┌─────┐ qr_0: |0>─┤ Cz ├┤ Ccx ├ └─┬──┘└──┬──┘ qr_1: |0>───┼──────┼─── │ │ qr_2: |0>───┼──────┼─── ┌──┴──┐┌──┴──┐ cr_0: 0 ╡ ╞╡ ╞ │ = 1 ││ = 3 │ cr_1: 0 ╡ ╞╡ ╞ └─────┘└─────┘ ``` ### What is the expected behavior? The mpl and latex drawers draw these correctly: ![image](https://user-images.githubusercontent.com/8622381/56842662-b4740a00-6865-11e9-961c-f81ffbc17e71.png) ![image](https://user-images.githubusercontent.com/8622381/56842667-bccc4500-6865-11e9-827b-5a125ed6da06.png) Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the Qiskit/qiskit codebase. Here's the problem: coupling_map.subgraph() creates extra nodes Trying to get a subgraph of this coupling map: ```py from qiskit.test.mock import FakeMumbai from retworkx.visualization import mpl_draw backend = FakeMumbai() cmap = CouplingMap(backend.configuration().coupling_map) mpl_draw(cmap.graph) ``` <img width="418" alt="image" src="https://user-images.githubusercontent.com/8622381/125465693-39b6c29f-bf4e-4399-8fac-7fa82acd0a50.png"> If I use retworkx directly to get the subgraph on 9 nodes, it gives me this which is correct I think: ```py mpl_draw(cmap.graph.subgraph([0, 1, 4, 7, 10, 12, 15, 18, 17])) ``` ![image](https://user-images.githubusercontent.com/8622381/125466722-037600b3-f217-48c7-9f71-f93bc08d3ef7.png) But if I do the same using the CouplingMap API I get this. There are incorrect nodes added here: ```py cmap.subgraph([0, 1, 4, 7, 10, 12, 15, 18, 17]).draw() ``` ![image](https://user-images.githubusercontent.com/8622381/125466756-aba38feb-114b-47c2-acbe-959abc7f319d.png) @mtreinish says this is due to a difference in how networkx and retworkx implement `.subgraph()`. But I like the retworkx output because it numbers nodes as 0-k, and that is consistent with how coupling maps in qiskit are numbered (i.e. no "holes"). So I think something just needs to change here to remove the extra nodes. If we provide an option to keep the original node numberings, I'd be fine with that, but I'm not sure whether Qiskit can actually work with such a coupling map object. The best route I see is to remap the node numbers in the same order (smallest to 0, largest to k). Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Setting log_format in config file results in error (and no format changes) Setting c.NotebookApp.log_format results in an error. The culprit is line 168 in config/application.py: ``` python _log_formatter = LevelFormatter(new, datefmt=self._log_datefmt) ``` Which should be: ``` python _log_formatter = LevelFormatter(new, datefmt=self.log_datefmt) ``` with no underscore before "log_datefmt." Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Commit 1ea3ddc6 breaks the compile command Prior to commit 1ea3ddc6 the *compile_commands.json* output from the config phase looks like this: ``` "command": "cc -Isrc/lib/libast/e416224@@ast@sta -Isrc/lib/libast -I../src/lib/libast -I. -I../ ``` I've omitted the subsequent args because they aren't relevant. With commit 1ea3ddc6 that same command looks like this: ``` "command": "cc -Isrc/lib/libast/e416224@@ast@sta -Isrc/lib/libast -I../src/lib/libast -I -I../ ``` **Notice that `-I.` has become `-I`** This breaks our build because a dynamically constructed header placed in the build root dir is no longer found. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the jupyterlab/jupyterlab codebase. Here's the problem: Watch mode to auto-compile extensions in active development First off, congratulations on JupyterLab. It's a great piece of software and I've loved working with it so far! I'm trying to build an extension not too different from https://github.com/jupyterlab/jupyterlab-google-drive. I'm having a hard time finding a good build process for rapid iteration on the extension and I've spend some time looking around for suggestions, but haven't found any. I set up an npm script which does a babel compile whenever my source changes, but I find I have to do the following each time I want to verify a change: 1. Kill `jupyter lab` process 2. Run `jupyter lab build` 3. Start `jupyter lab` process (opens a new tab) At this point, my extension changes are shown. I'm wondering if there is a watch mode I can run or some way to symlink my directory like `npm link` for example to make this process more seamless. Ideally without having to restart `jupyter lab` so I can keep working in my same tab. I'm happy to contribute docs or help set up a watch process if there isn't anything currently in place on either front. Thanks in advance. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Global Gradient calculation is turned off during validation step. If an error occurs during the validation step, the tradition calculation is turned off for the runtime, you have to either specifically enable it or restart runtime! Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Issues with man pages I've run into issues with how ipython installs its man pages: - Since 0.13, the man pages are no longer gzipped when installed - I just wanted to check if this is intentional? - When installing ipython with Python 3.2, the man pages are not installed - is this normal? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Progress Bar for large model loading ### Feature request Add progress bars for large model loading from cache files. ### Motivation Most of the time, model loading time will be dominated by download speed. However, for very large models we will often first download the checkpoints, then during runtime simply load them from cache. For models like Bloom however, it can take upwards of 100 minutes to load the model into RAM. During this time, there is no feedback to the user, even with verbosity set to debug. This can be frustrating as the only way to check progress is by checking system utilisation through `top`. ### Your contribution Happy to help if I am pointed to the relevant file or files! I don't think the progress bar would need to be extremely accurate, just some indication that something is happening. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: objc freestanding sanitycheck failed Header stdio.h isn't available on the freestanding environment, https://github.com/mesonbuild/meson/blob/7b9c348102792030859ed0001a51416506a0a092/mesonbuild/compilers/objc.py#L44 https://en.cppreference.com/w/cpp/freestanding Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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 underscore prefix from (almost) all files <!-- ⚠ 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? As we are transitioning from relative imports to absolute imports: ```python from ._module import Class ---> from qiskit.module import _module ``` We are introducing code like: ```python circuit = _quantumcircuit.QuantumCircuit() ``` ... this code is telling me that I want a `QuantumCircuit` class from an internal/private `_module`, but QuantumCircuit is not internal nor private. The concept of internal classes has been diffused during all this time, and I don't think we have this concept anymore, at least not in the vast majority of the files. So in order to keep code cleaner, I'd suggest to remove underscore prefix from all the files that we have doubts about its domain and files we know they are meant to be used by other components (I'd say all of them). This is somewhat of a large change, mostly style related so I'm labeling this issue as `discussion` just in case someone has different views. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Merge task responds to a merge trigger ## Current behavior *Please describe how the feature works today* A merge task will run even if all upstream tasks are skipped. ## Proposed behavior *Please describe your proposed change to the current behavior* If there are no tasks proceeding, a merge task should be skipped as well. ## Example *Please give an example of how the enhancement would be useful* If I have an ETL process with 3 conditional Transform tasks that aren't met, the downstream Load dependency should be skipped, since none of its upstream Transform tasks were completed. A merge task with only skipped ancestors should not be run. If I have an upstream conditional that is not met, the downstream dependency should be considered as also not met. Trigger to be implemented (courtesy of @cicdw): ``` def merge_trigger(upstream_states): if all(state.is_skipped() for state in upstream_states): raise signals.SKIP("All upstreams skipped") elif not all(state.is_successful() for state in upstream_states): raise signals.TRIGGERFAIL( 'Trigger was "all_successful" but some of the upstream tasks failed.' ) return True ``` Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the ipython/ipython codebase. Here's the problem: Uninformative error when saving notebook to HTML w/o pygments If you try to save your Notebook to HTML (or do "print preview") and pygments is not installed, you get a very unhelpful 500 error page. When I looked at stdout/err from notebook I see: ``` ERROR:tornado.access:500 GET /nbconvert/html/XXX.ipynb?download=false (XXX) 3.13ms referer=XXX WARNING:tornado.general:500 GET /nbconvert/html/XXX?download=false (XXX): Could not construct Exporter: No module named pygments.formatters ERROR:tornado.access:{ "Accept-Language": "en-US,en;q=0.8", "Accept-Encoding": "gzip,deflate,sdch", "Connection": "keep-alive", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8", "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36", "Host": "XXXX:8888", "Referer": "XXXX.ipynb", "Cache-Control": "max-age=0" } ``` The solution was to install `pygments`, but it would be nice if the HTML page said that rather than a 500 error. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the docker/compose codebase. Here's the problem: docker-compose up assumes --no-build It seems if I try to run docker-compose up with a yml that uses `build: .` and the image does not already exist, it acts like --no-build is passed. This is on version 1.3.1 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 huggingface/transformers codebase. Here's the problem: Option to change Ray's gridsearch scope # 🚀 Feature request It would be great if we can get more control over how Ray is selecting the best trial in a hyperparameter search. Currently, the default value for [`get_best_trial`](https://docs.ray.io/en/latest/tune/api_docs/analysis.html#ray.tune.ExperimentAnalysis.get_best_trial) is used here: https://github.com/huggingface/transformers/blob/7c5d79912a21880ce13d77881940458e90d98917/src/transformers/integrations.py#L299 namely `scope="last"`. So for each trial, it will simply take the _last_ checkpoint of that trial, and use its performance to compare with the other trials. This is not always ideal as it may very well be that some trials converge sooner than other and than overfit, leading to poor evaluation scores in their last checkpoints. Fortunately, Ray allows other options, such as `"all"`, which takes the best checkpoint instead of the last, of each trial and compares those. ## Motivation Currently there is no way to pass this through to Ray from within `transformers` as I can tell, yet it is an important aspect of hyperparameter search. ## Your contribution I can work on this if requested, although I am still looking for input how to best tackle this. One could simply add an argument to TrainingArguments, e.g. `ray_scope`, and then change this line https://github.com/huggingface/transformers/blob/7c5d79912a21880ce13d77881940458e90d98917/src/transformers/integrations.py#L299 to ```python best_trial = analysis.get_best_trial(metric="objective", mode=direction[:3], scope=trainer.args.ray_scope) ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Deploy Conan develop branch on test.pypi.org To help us debug your issue please explain: Hi! My proposal here is return to use test.pypi.org (used until Conan 0.4.1) when merging a new PR into develop branch. I see no difficult installing Conan on my machine running `pip install .` but for who wants to install the latest version (non-stable) without git, it could be an good option. For example, bincrafters-package-tools is uploaded to test.pypi.org for every new change in master branch (we follow github flow), only tags are uploaded to pypi.org. That flow helped me to find many bugs, including missing files in the package. The version released could be incremental, using the suffix dev as well. Conan Version: ANY OS: ANY - [X] I've read the [CONTRIBUTING guide](https://raw.githubusercontent.com/conan-io/conan/develop/.github/CONTRIBUTING.md). - [X] I've specified the Conan version, operating system version and any tool that can be relevant. - [X] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Audit Log for Connections/Variables update ### Description We have audit logs for major actions in Airflow except for Connection/Variables creation, update, and deletion ### Use case/motivation Connections and variables form the primary component of DAGs. Having a track of who changed what when will come in handy when troubleshooting ### Related issues _No response_ ### Are you willing to submit a PR? - [X] Yes I am willing to submit a PR! ### Code of Conduct - [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md) Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the conda/conda codebase. Here's the problem: Add tests and improve behavior for spaces in paths Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the apache/airflow codebase. Here's the problem: Update TaskFlow API example to use `@dag` decorator **Description** Update https://github.com/apache/airflow/blob/master/airflow/example_dags/tutorial_taskflow_api_etl.py tp use `@dag` decorator instead of leveraging context manager to make it more TaskFlow-y. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Cannot import RobertaPreTrainedModel ## Environment info I tried with both transformers 3.5.1 and 4.6.1. ### Who can help Maybe @julien-c since they contributed RoBERTa. ## Information I want to derive my own class from RobertaPreTrainedModel, but I cannot import that class like I can import e.g. BertPreTrainedModel or AlbertPreTrainedModel. More specifically, ```from transformers import BertPreTrainedModel``` and ```from transformers import AlbertPreTrainedModel``` works, but ```from transformers import RobertaPreTrainedModel``` returns `ImportError: cannot import name 'RobertaPreTrainedModel'`. Is this the intended behavior or could it be a bug? ## To reproduce Try `from transformers import RobertaPreTrainedModel` ## Expected behavior The RobertaPreTrainedModel class should be imported like it works for other transformers. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: error reporting still broken at 0.24 After updating to 0.24 to fix https://github.com/GoogleCloudPlatform/google-cloud-python/issues/3167 I'm still unable to report exceptions. Ubuntu xenial w/ Python 3.5.2 ```python client.report_exception(http_context=error_reporting.build_flask_context(flask.request)) ``` On google-cloud-error-reporting <0.23 the above line works fine. At 0.24 I get: ```python Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/cloud/error_reporting/client.py", line 347, in report_exception Apr 1 15:52:51 user=user) Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/cloud/error_reporting/client.py", line 276, in _send_error_report Apr 1 15:52:51 self.report_errors_api.report_error_event(error_report) Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/cloud/error_reporting/_gax.py", line 75, in report_error_event Apr 1 15:52:51 ParseDict(error_report, error_report_payload) Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/protobuf/json_format.py", line 384, in ParseDict Apr 1 15:52:51 parser.ConvertMessage(js_dict, message) Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/protobuf/json_format.py", line 415, in ConvertMessage Apr 1 15:52:51 self._ConvertFieldValuePair(value, message) Apr 1 15:52:51 File "/usr/local/lib/python3.5/dist-packages/google/protobuf/json_format.py", line 501, in _ConvertFieldValuePair Apr 1 15:52:51 raise ParseError('Failed to parse {0} field: {1}'.format(name, e))" ``` Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: virtualenv generator with `set -u` leads to unbound variable failure Conan 1.9.0, ubuntu 16.04 If a package sets env_info to a list (so that [tools.environment_append](https://docs.conan.io/en/latest/reference/tools.html?highlight=environment_append#tools-environment-append) will prepend it with a delimter, the virtualenv generator produces an assignment like: `PYTHONPATH=".../release/package/5ab84d6acfe1f23c4fae0ab88f26e3a396351ac9/python":$PYTHONPATH` If there is no current value in that variable, and `set -u` is in effect, this will cause the shell to error out with `bash: PYTHONPATH: unbound variable` To fix this, the virtualenv generators should explicitly use a conditional expansion like ${PYTHONPATH:-}, that can substitute to nothing if the variable is unset (even with set -u, since this was explicitly requested). But since I think it would also be nice to not get a junk trailing delimiter when there's nothing to append, I suggest: `val1:val2${NAME+:$NAME}` Despite being a little fancy, `${VAR:-}` and `${VAR+}` are portable posix sh substitutions, not bashisms (see [section 26.2 Parameter Expansion](http://pubs.opengroup.org/onlinepubs/009695399/utilities/xcu_chap02.html#tag_02_06_02)) - [x] I've read the [CONTRIBUTING guide](https://raw.githubusercontent.com/conan-io/conan/develop/.github/CONTRIBUTING.md). - [x] I've specified the Conan version, operating system version and any tool that can be relevant. - [x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Implement Virtual Package Plugin Hook and Plugins ### Checklist - [X] I added a descriptive title - [X] I searched open requests and couldn't find a duplicate ### Why is this needed? #### Virtual Package Hooks An implementation of virtual packages via the plugin system would be a good use-case for the new plugin infrastructure, since it will enable other virtual packages to be able to be utilized without requiring direct changes to the `conda` codebase; we will need to create hooks for these first. #### Virtual Package Plugins [Virtual packages defined by conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-virtual.html) can be implemented as core plugins under the `conda.plugins.*` namespace and registered directly in `conda.base.context.get_plugin_manager`. The virtual packages plugins will be shipped by default with `conda`, as an initial set of officially `conda`-developed plugins. ### What should happen? Hooks that enable virtual package plugins will be created in the [`plugins/__init__.py` file](https://github.com/conda/conda/blob/feature/plugins/conda/plugins/__init__.py). After that,`index.py` will be refactored to accommodate for usage of plugins (vs hard-coded virtual package detection), and we will develop separate plugin modules for our currently-supported virtual packages (_i.e._, Linux, CUDA, MacOS, Windows) which will live in the [plugins directory](https://github.com/conda/conda/tree/feature/plugins/conda/plugins). These will then get registered directly in `conda.base.context.get_plugin_manager` instead of via entrypoints. ### Additional Context This work is a continuation of the initial plugin implementation [here](https://github.com/conda/conda/pull/11435) (connected to issue https://github.com/conda/conda/issues/11112). Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the conda/conda codebase. Here's the problem: Add automatic error report uploads Rather than asking users to report unexpected errors on the github issue tracker, offer to post the error to a private resource accessible by the conda core team. The posted content should be anonymous. It should only include the error stack trace and the contents of `conda info`. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: logging basic configuration level: INFO vs. WARNING (usability with W&B) Thanks for the amazing package! I am having a great time using it. # Issue Recently, I have been playing around with the weights and biases (W&B) logging functionality and I noticed that I was getting a lot of logging messages in my jupyter notebook while training my model (every epoch I got new messages). When I looked into `logging.__init__.py`, the logging basic configuration was set with: `logging.basicConfig(level=logging.INFO)` However, that means a lot of INFO messages are being printed from W&B's use of the logger (e.g. when the RunManager modifies files). # Potential Solution To disable this, I switched the logging basic configuration in `logging.__init__.py` to: `logging.basicConfig(level=logging.WARNING)` Would this be a useful addition in general to the package or should I just keep this change local? Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: resubmitted tasks doesn't have same session name If I understand correctly, a task gets a new msg_id when you call client.resubmit(msg_id). I noticed that the 'cloned' task seems to have a random session name. I would suggest to take over all cutomizable attributes: session, username, retries, after, ... in order to let the resubmitted task behave like the original one. One side effect for me would be to delete the original task after the resubmitted one took it's place. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Can't pass parameters to a Clock unless they have default values ## Description *A clear description of the bug* I would like to create a flow on a schedule, passing in default parameters. Currently this fails unless all parameters have default values. ## Expected Behavior *What did you expect to happen instead?* Passing parameters should be allowed even if they do not have defaults - we should be able to resolve the following example ## Reproduction *A minimal example that exhibits the behavior.* ```from prefect import task, Parameter, Flow from prefect.schedules import Schedule from prefect.schedules.clocks import CronClock @task def add(a, b): return a + b schedule = Schedule(clocks=[ CronClock( cron=f"* * * * *", parameter_defaults={ 'a': 1, } ) ]) with Flow('flow', schedule=schedule) as flow: a = Parameter('a') b = Parameter('b', default=1) result = add(a, b) flow.register() ``` ## 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 conan-io/conan codebase. Here's the problem: Add "keep_permissions" option to tools.get() A nice enhancement to the tools.get() high level wrapper function would be allowing the user to keep permissions when the unzip process happens. This is really useful when downloading compilers or other tools that need to be marked as executable. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the conan-io/conan codebase. Here's the problem: [bug] compiler.base.runtime is not set based on build_type when using Visual Studio as the base compiler <!-- Please don't forget to update the issue title. Include all applicable information to help us reproduce your problem. To help us debug your issue please explain: --> Currently, `compiler.runtime` is implicitly set based on the `build_type` being used. When using `compiler=Intel` and Visual Studio for a base compiler, we expect `compiler.base.runtime` to be set based on the build_type as well. This is not the case, though, and it needs to be set explicitly on the command line or conditionally set directly in the recipe (which I do not think is recommended). There are easy workarounds to this, but it makes using the Intel compiler settings not as straight forward. ### Environment Details (include every applicable attribute) * Operating System+version: Windows 10 * Conan version: 1.21.0 * Python version: 3.7.3 ### Steps to reproduce (Include if Applicable) Start from a new bare recipe `conan new test/1.2.3 -b` Create a package from this bare recipe with `compiler=Intel`, `compiler.base="Visual Studio"`, `build_type`, and compiler version settings `conan create . -s compiler=intel -s compiler.version=19 -s compiler.base="Visual Studio" -s compiler.base.version=15 -s build_type=Release` The following error is received `ERROR: test/1.2.3: 'settings.compiler.base.runtime' value not defined` Meanwhile running with `Visual_Studio` as the compiler implicitly sets the runtime and succeeds `conan create . -s compiler="Visual Studio" -s compiler.version=15 -s build_type=Release` > [settings] arch=x86_64 arch_build=x86_64 build_type=Release compiler=Visual Studio compiler.runtime=MD compiler.version=15 Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Bloch Sphere Visualization doesn't do anything with non-GUI backends <!-- ⚠ If you do not respect this template, your issue will be closed --> <!-- ⚠ Make sure to browse the opened and closed issues --> ### Informations - **Qiskit Terra version**: latest master (but should effect released versions too) - **Python version**: 3.7 - **Operating system**: Linux ### What is the current behavior? When calling `qiskit.tools.visualization.plot_bloch_vector()` it unconditionally calls show() on the figure to get an interactive 3d visualization of the bloch sphere for the provided vector. However if you're using a non-GUI matplotlib backend this doesn't have a user visible effect. All that happens is that matplotlib will emit a warning like: `lib/python3.5/site-packages/matplotlib/figure.py:448: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.` This comes up particularly if running on a system that doesn't have X or a graphical interface installed. All that happens is the warning is displayed and the script exits without failure. ### Steps to reproduce the problem Call `qiskit.tools.visualization.plot_bloch_vector()` on a system with matplotlib configured with a non-GUI backend. ### What is the expected behavior? The visualization is saved to disk somewhere, or the function returns the PIL.image object (or something else that represents the visualization) ### Suggested solutions Add a filename flag and/or add a return for the function. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: possible mistake in documentation Looking at description of the parameter "decoder_input_ids" in "forward" method of BartForConditionalGeneration/T5ForConditionalGeneration, I see following: BartForConditionalGeneration: decoder_input_ids - ... For translation and summarization training, decoder_input_ids should be provided. If no decoder_input_ids is provided, the model will create this tensor by shifting the !!INPUT_IDS!! to the right for denoising pretraining following the paper. T5ForConditionalGeneration: decoder_input_ids - ... To know more on how to prepare decoder_input_ids for pretraining take a look at T5 Training. If decoder_input_ids and decoder_inputs_embeds are both unset, decoder_input_ids takes the value of !!INPUT_IDS!!. Looks like there should be LABELS instead of INPUT_IDS. Thanks, @patrickvonplaten, @patil-suraj Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the googleapis/google-cloud-python codebase. Here's the problem: Pubsub: clients emit pending deprecation warnings (See [Google Group](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/cloud-pubsub-discuss/A53nuoc3Eb4/LH6gwaXfDgAJ) ) With the Python pubsub package v 0.39.0, a simple call to pubsub_v1.SubscriberClient() gives warnings from deep in Google code ``` publisher/client.py:89: PendingDeprecationWarning: The `channel` argument is deprecated; use `transport` instead. ... subscriber/client.py:83: PendingDeprecationWarning: The `channel` argument is deprecated; use `transport` instead. ... ``` This apparently incorrect channel is created inside Google code, e.g. `google.cloud.pubsub_v1.subscriber.client.Client#__init__` Although keeping ahead of deprecation can be challenging, Google's _own_ code should avoid warnings and do whatever Google says is the official way. Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Cleanup stopped containers in docker agent Currently containers that finish aren't cleaned up, and will build up over time. We should make use of the `AutoRemove` option on `HostConfig` when starting a container to automatically delete containers after they've completed. This requires docker engine api version >= 1.25, which came out in Jan 2017 - given that it's been around for a few years I think we can apply this universally. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: Inverting a quantum circuit <!--- Provide a general summary of the issue in the Title above --> I can create a circuit for generating arbitrary quantum superposition with `initialize()` function. I know there is a call to `inverse()` function within the `initialize()`. So, it should be easy to do that (just do not execute that call to `inverse()`). But I cannot find a way to inverse a circuit I obtain from the `initialize()` nor for any quantum circuit that I have. ## Expected Behavior <!--- If you're describing a bug, tell us what should happen --> <!--- If you're suggesting a change/improvement, tell us how it should work --> Access to `inverse()` function, or, at least an example of using `CompositeGate` that supports operation to invert the gate. ## Current Behavior <!--- If describing a bug, tell us what happens instead of the expected behavior --> <!--- If suggesting a change/improvement, explain the difference from current behavior --> There seems to be no test case and examples of using `CompositeGate` from the `initialize()`. ## Possible Solution <!--- Not obligatory, but suggest a fix/reason for the bug, --> <!--- or ideas how to implement the addition or change --> ## Steps to Reproduce (for bugs) <!--- Provide a link to a live example, or an unambiguous set of steps to --> <!--- reproduce this bug. Include code to reproduce, if relevant --> 1. 2. 3. 4. ## Context <!--- How has this issue affected you? What are you trying to accomplish? --> <!--- Providing context helps us come up with a solution that is most useful in the real world --> ## Your Environment <!--- Include as many relevant details about the environment you experienced the bug in --> * Version used: 0.5.2 * Environment name and version (e.g. Python 3.6.1): Python 3.6.x * Operating System and version: MacOSX Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: no validity check on Target construction ### Environment - **Qiskit Terra version**: - **Python version**: - **Operating system**: ### What is happening? It's possible to build a Target where the Instruction does not match the number of qubits it's being added to. ### How can we reproduce the issue? For example here I add a 1-qubit gate to a two-qubit tuple. ```py from qiskit.transpiler import Target, InstructionProperties from qiskit.circuit.library import RZGate from qiskit.circuit import Parameter θ = Parameter('θ') rz_props = { (0, 1): InstructionProperties(duration=0, error=0) } target = Target() target.add_instruction(RZGate(θ), rz_props, name='rz') ``` ### What should happen? raise Error ### Any suggestions? _No response_ Can you help me debug this systematically and explain your reasoning?


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

[User] I'm having an issue with the PrefectHQ/prefect codebase. Here's the problem: Proposal: make upstream inputs have precedance over cached_inputs Currently, the `TaskRunner.get_task_inputs()` method will load upstream inputs, then overwrite that dict with any cached inputs on the task. I'd like to propose reversing that order, so first cached inputs are loaded, then upstream inputs overwrite them. Let's say task A runs and then task B wants to be retried. If I (manually) rerun task A, then my expectation would be that task B would use A's *new* result, not the old one that task B cached. In other words, while it's a useful and important Prefect feature that *B* does the caching of *A's* result, this is a case where that would go against my expectation, since B's cache no longer matches A's result. This isn't a fully baked recommendation, but I'd like to think through the above situation and see if it can/should be addressed. cc @cicdw Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: [question] RuntimeWarning while using python_requires In Conan 1.8, I am getting RuntimeWarning while using python_requires: ``` conan export . demo/test /home/sun/.conan/data/MyBase/1.7/demo/test/export/conanfile.py:1: RuntimeWarning: Parent module 'MyBase/1' not found while handling absolute import from conans import ConanFile, CMake, tools /home/sun/.conan/data/MyBase/1.7/demo/test/export/conanfile.py:2: RuntimeWarning: Parent module 'MyBase/1' not found while handling absolute import import os,sys .. .. ``` My base conan file is: ``` from conans import ConanFile, CMake, tools import os,sys, _scm = { "type" : "git", "url" : "auto", "revision" : "auto" } class MyBase(ConanFile): .. .. ``` To help us debug your issue please explain: - [x] I've read the [CONTRIBUTING guide](https://raw.githubusercontent.com/conan-io/conan/develop/.github/CONTRIBUTING.md). - [x] I've specified the Conan version, operating system version and any tool that can be relevant. - [x] I've explained the steps to reproduce the error or the motivation/use case of the question/suggestion. Can you help me debug this systematically and explain your reasoning?


[System] You are an expert software 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: initial_layout cannot be used in compile with circuits of differing qubit number <!-- ⚠ 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? You can not use an `initial_layout` when circuits with differing numbers of qubits are input to compile. This is true even the circuits are smaller than the size of the layout passed, i.e. the layout is valid for the subset of qubits in the smaller width circuits. ``` q = QuantumRegister(3,'q') c = ClassicalRegister(3) qc = QuantumCircuit(q, c) qc.h(q[0]) qc.cx(q[0], q[1]) qc.cx(q[1], q[2]) qc.measure(q, c) q = QuantumRegister(2,'q') c = ClassicalRegister(2) qc2 = QuantumCircuit(q, c) qc2.h(q[0]) qc2.cx(q[0], q[1]) qc2.measure(q, c) layout = [None, None, (QuantumRegister(3, 'q'), 0), (QuantumRegister(3, 'q'), 1), (QuantumRegister(3, 'q'), 2)] backend = IBMQ.get_backend('ibmqx4') qobj = compile([qc, qc2], backend, initial_layout = layout) ``` `MapperError: 'initial_layout qubit q[2] not in input DAGCircuit'` ### Steps to reproduce the problem ### What is the expected behavior? Given that we allow compiling circuits with different widths, I would expect that we can supply initial_layouts to these circuits. If we are not allowing this, then terra should throw the proper warning before trying to compile the circuits. ### Suggested solutions Can you help me debug this systematically and explain your reasoning?