why is bundle install hanging with no output

A silent `bundle install` is usually blocked on interactive input, such as a gem-source credentials prompt. Atlas's bash tool times the command out and explicitly calls out the interactive-input case, so the fix is a non-interactive flag rather than a larger timeout.

how do I stop rspec from hanging on binding.pry

A committed `binding.pry` stops an RSpec example and waits on stdin forever. Atlas indexes Ruby code by AST declarations using tree-sitter, so it can locate the `binding.pry` in the spec file that owns it, then surface a unified diff removing it for your approval.

how do I increase the timeout for a slow rspec suite in atlas

Retry the command with a larger timeout value in milliseconds, exactly as Atlas's timeout message instructs. Raising the timeout is the right move for a genuinely slow `bundle exec rspec` run, and the wrong move for a command blocked on interactive input.

difference between a hung ruby command and a slow one

A slow Ruby command finishes if you give it more milliseconds. A hung one is waiting on stdin and never finishes. Atlas's timeout message draws the line for you by stating the retry advice only applies when the command is not waiting for interactive input.

does atlas run bundler and rubocop commands without asking

No. Every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs, so a `bundle install` or `bundle exec rubocop` invocation is checked against your rules first. You see the command, including any non-interactive flags, before it executes.

atlas says user aborted the command in ruby

The metadata line User aborted the command means you interrupted the run yourself, not that the command timed out or hung. Atlas surfaces it precisely so your own Ctrl-C is never misdiagnosed as a blocked Bundler or RSpec process.

can atlas undo an edit it made to my Gemfile or spec files

Yes. Atlas snapshots file changes as git patches so edits can be diffed and rolled back, and it computes a unified diff for every file edit and surfaces it for approval before writing to a Gemfile, a Rakefile, or anything under `spec/`.

Diagnose a hanging or long-running command in Ruby with Atlas (2026)

In Ruby, a command that never returns is usually blocked on stdin, not slow. Atlas races every bash command against a timeout, and when the timeout expires it tells you exactly what happened and what to do: retry with a larger timeout if the command is expected to take longer and is not waiting for interactive input. That second clause is the diagnosis. A `bundle install` waiting on a credentials prompt, or an `rspec` run stopped at a `binding.pry`, will never finish no matter how long you wait, so Atlas points you at the non-interactive flags instead of a bigger number.

Why does my Ruby command hang forever in the terminal?

A hanging Ruby command is almost always blocked on standard input, not slow. Bundler asks for gem-source credentials, RSpec stops at a `binding.pry` breakpoint, and a Rakefile task waits on a yes-or-no confirmation. Atlas separates the two cases in 2026 by racing every bash command against a timeout.

Atlas runs Ruby commands through its bash tool, which races the process against a timeout in milliseconds. When the timeout expires, Atlas does not simply say the command failed. It reports what happened and what to do: retry with a larger timeout if the command is expected to take longer and is not waiting for interactive input. The condition matters more than the advice. A `bundle exec rspec` suite that legitimately takes four minutes will finish if you give it enough milliseconds. A `bundle install` sitting at a Gemfile source credentials prompt will not finish in four minutes or four hours, because nothing is going to type the password. Atlas explicitly calls out the interactive-input case so a Ruby developer stops raising the timeout and starts adding a non-interactive flag. Common Ruby offenders include RSpec examples that reached a `binding.pry`, a `rails db:migrate` waiting on a destructive-change confirmation, and a `gem push` prompting for OTP.

How do I tell a slow RSpec suite from a blocked one with Atlas?

Atlas prints a shell_metadata block when a Ruby command is killed, and that block is the whole diagnosis. Read it before you change anything. Atlas's message splits the outcome into 2 paths: the RSpec suite is genuinely slow, or it is silently blocked on stdin waiting for input that never arrives.

The read is mechanical. Run the command with Atlas's bash tool, let it hit the timeout, then read the shell_metadata block in the output. Atlas's message distinguishes two paths. Path one: the command is expected to take longer and is not waiting for interactive input, so retry with a larger timeout value in milliseconds. That is the right call for a slow `bundle exec rspec spec/` run over a few thousand examples, or a `bundle exec rubocop` pass over a large app. Path two: the command is waiting on input, in which case a larger timeout changes nothing. That is the right read when `bundle install` stalls with no progress lines, or when an RSpec example stopped emitting dots partway through the suite. Atlas also distinguishes your own interrupt from a timeout: if you aborted it yourself, the metadata says User aborted the command, so a Ctrl-C is never mistaken for a hang.

What non-interactive flags stop Bundler and RSpec from prompting?

When Atlas reports that a Ruby command is blocked on interactive input, the fix is a non-interactive flag, not a bigger timeout. Re-run the command through Atlas's bash tool using the tool's non-interactive flags. The 3 documented forms are -y, --no-input, and CI mode, so Bundler cannot stop and prompt.

The documented Atlas step is to re-run with the tool's non-interactive flags (-y, --no-input, CI mode) so it cannot prompt. In a Ruby project that means letting Bundler take its credentials from the environment rather than a terminal prompt, and running the suite in a mode where nothing pauses to ask. Atlas's bash tool is permission-gated like every other Atlas tool call, checked against allow, ask, and deny rules before it runs, so you see the exact command with its new flags before Atlas re-executes it. After the flag is added, re-run `bundle exec rspec` through bash and read the output. If the command now completes, or fails with a real error instead of silence, the hang was input, not duration. If it still hits the timeout while producing steady output, the suite is genuinely slow and the correct move is a larger timeout in milliseconds.

How do I find the binding.pry or gets call that is blocking the Ruby run?

Atlas finds the blocking Ruby call itself, not just the symptom. Atlas searches code with hybrid semantic and keyword retrieval fused by reciprocal rank fusion, and indexes code by AST declarations using tree-sitter rather than blind line windows, so a stray binding.pry in a spec file surfaces in 2026 as a real declaration.

Once Atlas has told you a Ruby command is blocked on stdin, the next question is which line is doing the blocking. Atlas reads the files with its read tool and locates candidates with search. Because Atlas indexes by AST declarations using tree-sitter, a `gets` inside a Rakefile task or a `STDIN.gets` inside a service object is returned in the context of the method that owns it, not as an orphan line. Hybrid semantic and keyword retrieval fused by reciprocal rank fusion means you can describe the behavior (a task that waits for confirmation) as well as grep the literal token. In an RSpec suite the usual culprits are a committed `binding.pry` in `spec/models/`, a `spec_helper.rb` hook that opens a prompt, or a support file that shells out to an interactive command. Atlas reads them and shows you the line.

Is it safe to let Atlas re-run a stuck Ruby command?

Yes, and Atlas enforces it at 2 layers. Every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs, so a re-run of bundle exec rspec with new flags is shown to you first. Atlas also computes a unified diff for every file edit and surfaces it for approval before writing.

Diagnosing a hang in Ruby often ends in an edit: deleting a committed `binding.pry`, adding a non-interactive option to a Rakefile task, or adjusting a `spec_helper.rb` hook. Atlas does not make those edits silently. Atlas computes a unified diff for every file edit and surfaces it for approval before writing, and it snapshots file changes as git patches so any edit can be diffed and rolled back. On the command side, the permission layer checks each bash invocation against allow, ask, and deny rules before it runs, which means the retried `bundle exec rspec` with a larger timeout, or the `bundle install` with a non-interactive flag, is a command you approved rather than one Atlas chose alone. Atlas also reads git branches, status, and diffs, so you can confirm the change to your Gemfile or spec files before it becomes a commit.

Step by step

01Run the Ruby command through Atlas's bash tool, for example `bundle exec rspec spec/`, and let it run against the timeout rather than killing it yourself.
02When the command is killed, read the shell_metadata block in the bash output. That block, not your intuition, is the diagnosis.
03Decide from Atlas's message whether the command is genuinely slow or blocked: Atlas explicitly calls out the interactive-input case, and says to retry with a larger timeout only if the command is not waiting for interactive input.
04If the Ruby command is blocked, re-run it with the tool's non-interactive flags (-y, --no-input, CI mode) so Bundler or RSpec cannot stop at a prompt.
05If the command is genuinely slow, retry with a larger timeout value in milliseconds, exactly as Atlas's message instructs, so a long `bundle exec rspec` run is not killed mid-suite.
06If you aborted the run yourself, expect the metadata to say User aborted the command, which distinguishes your interrupt from a real timeout.
07Use Atlas's read tool on the suspect file (a spec under `spec/`, a Rakefile task, or `spec_helper.rb`) to find the `binding.pry` or `gets` that was blocking.
08Remove or guard the blocking call, review the unified diff Atlas surfaces before it writes, then re-run `bundle exec rspec` and `bundle exec rubocop` through bash to confirm the project is clean.

Frequently asked questions

why is bundle install hanging with no output: A silent `bundle install` is usually blocked on interactive input, such as a gem-source credentials prompt. Atlas's bash tool times the command out and explicitly calls out the interactive-input case, so the fix is a non-interactive flag rather than a larger timeout.
how do I stop rspec from hanging on binding.pry: A committed `binding.pry` stops an RSpec example and waits on stdin forever. Atlas indexes Ruby code by AST declarations using tree-sitter, so it can locate the `binding.pry` in the spec file that owns it, then surface a unified diff removing it for your approval.
atlas bash command timed out what does that mean: When an Atlas bash command times out, Atlas reports what happened and what to do: retry with a larger timeout if the command is expected to take longer and is not waiting for interactive input. Read the shell_metadata block first to decide which case you are in.
how do I increase the timeout for a slow rspec suite in atlas: Retry the command with a larger timeout value in milliseconds, exactly as Atlas's timeout message instructs. Raising the timeout is the right move for a genuinely slow `bundle exec rspec` run, and the wrong move for a command blocked on interactive input.
difference between a hung ruby command and a slow one: A slow Ruby command finishes if you give it more milliseconds. A hung one is waiting on stdin and never finishes. Atlas's timeout message draws the line for you by stating the retry advice only applies when the command is not waiting for interactive input.
does atlas run bundler and rubocop commands without asking: No. Every Atlas tool call is permission-gated against allow, ask, and deny rules before it runs, so a `bundle install` or `bundle exec rubocop` invocation is checked against your rules first. You see the command, including any non-interactive flags, before it executes.
atlas says user aborted the command in ruby: The metadata line User aborted the command means you interrupted the run yourself, not that the command timed out or hung. Atlas surfaces it precisely so your own Ctrl-C is never misdiagnosed as a blocked Bundler or RSpec process.
can atlas undo an edit it made to my Gemfile or spec files: Yes. Atlas snapshots file changes as git patches so edits can be diffed and rolled back, and it computes a unified diff for every file edit and surfaces it for approval before writing to a Gemfile, a Rakefile, or anything under `spec/`.

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