PythonImageAnalysis/troubleshooting.html at main · HenriquesLab/PythonImageAnalysis · GitHub

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    <title>Troubleshooting | So You Want To Do Image Analysis With Python</title>
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            <p class="page-kicker">Troubleshooting</p>
            <h1>When the computer has other ideas</h1>
            <p class="lead">
              This page exists for the moments when something absolutely should
              have worked and very much did not. Most beginner problems are
              recoverable and usually belong to a few repeat patterns.
            </p>
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          <section class="panel">
            <h2>Python does not seem to exist</h2>
            <ol class="step-list">
              <li>Try <code>python --version</code>, then <code>python3 --version</code>, then <code>py --version</code>.</li>
              <li>Close and reopen the terminal after installation.</li>
              <li>If the command is still not found, the issue is often PATH-related rather than a total install failure.</li>
            </ol>
            <pre><code>python --version
python3 --version
py --version</code></pre>
          </section>

          <section class="panel">
            <h2>A package installed, but import still fails</h2>
            <ol class="step-list">
              <li>Confirm the environment is activated.</li>
              <li>Run <code>python -c "import sys; print(sys.executable)"</code>.</li>
              <li>Install the package again inside that same environment.</li>
              <li>If using Jupyter, confirm the notebook kernel matches the environment you expect.</li>
            </ol>
            <pre><code>python -c "import sys; print(sys.executable)"
python -m pip list</code></pre>
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            <h2>Jupyter is behaving strangely</h2>
            <ol class="step-list">
              <li>Restart the kernel.</li>
              <li>Run all cells from the top.</li>
              <li>Check whether a variable from an earlier run is still lingering in memory.</li>
              <li>If needed, build a fresh notebook with the smallest working example.</li>
            </ol>
            <pre><code>jupyter lab
# then inside Jupyter:
# Kernel -> Restart Kernel
# Run -> Run All Cells</code></pre>
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          <section class="panel">
            <h2>napari or the plugin will not launch</h2>
            <ol class="step-list">
              <li>Confirm you are in the environment where napari was installed.</li>
              <li>Reinstall the plugin in that same environment.</li>
              <li>If the environment feels messy, create a fresh one rather than layering more fixes onto the old one.</li>
            </ol>
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            <h3>One reassuring pattern</h3>
            <p>
              When something fails, slow the problem down. Ask which environment
              is active, which command name works, and what exact error message
              appeared. Those three pieces solve a surprising number of issues.
            </p>
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