{
  "id": 545973,
  "title": "Submission Fails Due to Missing Modules",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/545973",
  "author_name": "",
  "post_date": "2024-11-13T04:48:47.067905100Z",
  "votes": null,
  "comment_count": 2,
  "views": 0,
  "content": "<p>Hello everyone,</p>\n<p>I'm encountering a recurring issue where my submissions fail due to missing modules. When I run the code myself in the Kaggle notebook, everything works fine, but it fails after submission.</p>\n<p>What I Tried:<br>\nIn the notebook, I use the following code to install the dependencies and add a custom path for importing:</p>\n<pre><code>!pip install --upgrade copick git+https://github.com/copick/copick-utils.git scikit-image cupy-cuda12x tqdm matplotlib --target=/kaggle/working/deps\n\n sys\nsys.path.append()\n\n copick\n</code></pre>\n<p>This code works perfectly when I run the notebook manually. However, after submission, the copick module isn’t found, and the run fails with a ModuleNotFoundError.</p>\n<p>Screenshot of the Error<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F8973638%2F76470d673a1862a70aa66a6ff67747a6%2FScreenshot%202024-11-13%20at%2005.35.21.png?generation=1731472764626410&amp;alt=media\" alt=\"\"></p>\n<p>My Questions:</p>\n<ul>\n<li>Do Kaggle submissions not support package installations with the --target option?</li>\n<li>Is there another way to include packages in the path so they’re recognized during submission?</li>\n<li>If you’ve encountered a similar problem, what solutions have worked for you?</li>\n</ul>\n<p>Thank you very much for your help!</p>",
  "messages": [
    {
      "id": "3044137",
      "postDate": "11/13/2024 04:48:47",
      "content": "<p>Hello everyone,</p>\n<p>I'm encountering a recurring issue where my submissions fail due to missing modules. When I run the code myself in the Kaggle notebook, everything works fine, but it fails after submission.</p>\n<p>What I Tried:<br>\nIn the notebook, I use the following code to install the dependencies and add a custom path for importing:</p>\n<pre><code>!pip install --upgrade copick git+https://github.com/copick/copick-utils.git scikit-image cupy-cuda12x tqdm matplotlib --target=/kaggle/working/deps\n\n sys\nsys.path.append()\n\n copick\n</code></pre>\n<p>This code works perfectly when I run the notebook manually. However, after submission, the copick module isn’t found, and the run fails with a ModuleNotFoundError.</p>\n<p>Screenshot of the Error<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F8973638%2F76470d673a1862a70aa66a6ff67747a6%2FScreenshot%202024-11-13%20at%2005.35.21.png?generation=1731472764626410&amp;alt=media\" alt=\"\"></p>\n<p>My Questions:</p>\n<ul>\n<li>Do Kaggle submissions not support package installations with the --target option?</li>\n<li>Is there another way to include packages in the path so they’re recognized during submission?</li>\n<li>If you’ve encountered a similar problem, what solutions have worked for you?</li>\n</ul>\n<p>Thank you very much for your help!</p>",
      "rawMarkdown": "Hello everyone,\n\nI'm encountering a recurring issue where my submissions fail due to missing modules. When I run the code myself in the Kaggle notebook, everything works fine, but it fails after submission.\n\nWhat I Tried:\nIn the notebook, I use the following code to install the dependencies and add a custom path for importing:\n\n```python\n!pip install --upgrade copick git+https://github.com/copick/copick-utils.git scikit-image cupy-cuda12x tqdm matplotlib --target=/kaggle/working/deps\n\nimport sys\nsys.path.append(\"/kaggle/working/deps\")\n\nimport copick\n```\n\nThis code works perfectly when I run the notebook manually. However, after submission, the copick module isn’t found, and the run fails with a ModuleNotFoundError.\n\nScreenshot of the Error\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F8973638%2F76470d673a1862a70aa66a6ff67747a6%2FScreenshot%202024-11-13%20at%2005.35.21.png?generation=1731472764626410&alt=media)\n\nMy Questions:\n- Do Kaggle submissions not support package installations with the --target option?\n- Is there another way to include packages in the path so they’re recognized during submission?\n- If you’ve encountered a similar problem, what solutions have worked for you?\n\nThank you very much for your help!",
      "votes": null
    },
    {
      "id": "3044345",
      "postDate": "11/13/2024 09:36:59",
      "content": "<p>Hey, this is a code competition so internet is turned off, so pip will not reach the PyPi servers. </p>\n<p>It has been discussed in other threads: <a href=\"https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427\" target=\"_blank\">https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427</a></p>\n<p>If you want an example I install copick offline in my notebook: <a href=\"https://www.kaggle.com/code/fnands/baseline-unet-train-submit\" target=\"_blank\">https://www.kaggle.com/code/fnands/baseline-unet-train-submit</a></p>",
      "rawMarkdown": "Hey, this is a code competition so internet is turned off, so pip will not reach the PyPi servers. \n\nIt has been discussed in other threads: https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427\n\nIf you want an example I install copick offline in my notebook: https://www.kaggle.com/code/fnands/baseline-unet-train-submit",
      "votes": null
    },
    {
      "id": "3045657",
      "postDate": "11/14/2024 16:50:47",
      "content": "<p>Hey <a href=\"https://www.kaggle.com/fnands\" target=\"_blank\">@fnands</a> Thanks for your help and these nice resources that helped me a lot. I managed to resolve the issue by implementing deps requirements in a Kaggle dataset. I also tried the package manager that worked 1/2 for me.</p>",
      "rawMarkdown": "Hey @fnands Thanks for your help and these nice resources that helped me a lot. I managed to resolve the issue by implementing deps requirements in a Kaggle dataset. I also tried the package manager that worked 1/2 for me.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3044345,
      "author_name": "fnands",
      "author_url": "",
      "post_date": "11/13/2024 09:36:59",
      "content": "<p>Hey, this is a code competition so internet is turned off, so pip will not reach the PyPi servers. </p>\n<p>It has been discussed in other threads: <a href=\"https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427\" target=\"_blank\">https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427</a></p>\n<p>If you want an example I install copick offline in my notebook: <a href=\"https://www.kaggle.com/code/fnands/baseline-unet-train-submit\" target=\"_blank\">https://www.kaggle.com/code/fnands/baseline-unet-train-submit</a></p>",
      "votes": null,
      "replies": [
        {
          "id": 3045657,
          "author_name": "drxc75",
          "author_url": "",
          "post_date": "11/14/2024 16:50:47",
          "content": "<p>Hey <a href=\"https://www.kaggle.com/fnands\" target=\"_blank\">@fnands</a> Thanks for your help and these nice resources that helped me a lot. I managed to resolve the issue by implementing deps requirements in a Kaggle dataset. I also tried the package manager that worked 1/2 for me.</p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "3044137": "Hello everyone,\n\nI'm encountering a recurring issue where my submissions fail due to missing modules. When I run the code myself in the Kaggle notebook, everything works fine, but it fails after submission.\n\nWhat I Tried:\nIn the notebook, I use the following code to install the dependencies and add a custom path for importing:\n\n```python\n!pip install --upgrade copick git+https://github.com/copick/copick-utils.git scikit-image cupy-cuda12x tqdm matplotlib --target=/kaggle/working/deps\n\nimport sys\nsys.path.append(\"/kaggle/working/deps\")\n\nimport copick\n```\n\nThis code works perfectly when I run the notebook manually. However, after submission, the copick module isn’t found, and the run fails with a ModuleNotFoundError.\n\nScreenshot of the Error\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F8973638%2F76470d673a1862a70aa66a6ff67747a6%2FScreenshot%202024-11-13%20at%2005.35.21.png?generation=1731472764626410&alt=media)\n\nMy Questions:\n- Do Kaggle submissions not support package installations with the --target option?\n- Is there another way to include packages in the path so they’re recognized during submission?\n- If you’ve encountered a similar problem, what solutions have worked for you?\n\nThank you very much for your help!",
    "3044345": "Hey, this is a code competition so internet is turned off, so pip will not reach the PyPi servers. \n\nIt has been discussed in other threads: https://www.kaggle.com/competitions/czii-cryo-et-object-identification/discussion/545427\n\nIf you want an example I install copick offline in my notebook: https://www.kaggle.com/code/fnands/baseline-unet-train-submit",
    "3045657": "Hey @fnands Thanks for your help and these nice resources that helped me a lot. I managed to resolve the issue by implementing deps requirements in a Kaggle dataset. I also tried the package manager that worked 1/2 for me."
  },
  "source": "meta"
}