{
  "id": 545006,
  "title": "Importing Zarr Into a Competition Notebook",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/545006",
  "author_name": "",
  "post_date": "2024-11-08T01:32:42.256249Z",
  "votes": 8,
  "comment_count": 7,
  "views": 0,
  "content": "<p>Took me a bit to figure this out.  Aside from no internet access, the asciitree dependency is what makes this more difficult than usual.  Here were my steps:</p>\n<ol>\n<li><p>Create a dataset that includes the zarr dependencies as described in the following notebook.  Basically this involves calling \"!pip download zarr\" from a new notebook and making a dataset from the output.<br>\n<a href=\"https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet\" target=\"_blank\">https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet</a></p></li>\n<li><p>Add the dataset to your notebook.  In step 4 below, I've named mine \"Zarr Dependencies Dataset\".</p></li>\n<li><p>Copy the asciitree directory to the working directory first to install it.  (Delete first so you can run the block more than once.)<br>\n!rm -rf /kaggle/working/asciitree-0.3.3<br>\n!cp -R /kaggle/input/zarr-dependencies-dataset/asciitree-0.3.3 /kaggle/working/.<br>\n!pip install --no-index /kaggle/working/asciitree-0.3.3/asciitree-0.3.3</p></li>\n<li><p>Then install zarr as described in the notebook above.<br>\n!pip install --no-index --find-links /kaggle/input/zarr-dependencies-dataset /kaggle/input/zarr-dependencies-dataset/zarr-2.18.3-py3-none-any.whl</p></li>\n<li><p>Import as normal.</p></li>\n</ol>\n<p>Hope this helps!</p>",
  "messages": [
    {
      "id": "3039379",
      "postDate": "11/08/2024 01:32:42",
      "content": "<p>Took me a bit to figure this out.  Aside from no internet access, the asciitree dependency is what makes this more difficult than usual.  Here were my steps:</p>\n<ol>\n<li><p>Create a dataset that includes the zarr dependencies as described in the following notebook.  Basically this involves calling \"!pip download zarr\" from a new notebook and making a dataset from the output.<br>\n<a href=\"https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet\" target=\"_blank\">https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet</a></p></li>\n<li><p>Add the dataset to your notebook.  In step 4 below, I've named mine \"Zarr Dependencies Dataset\".</p></li>\n<li><p>Copy the asciitree directory to the working directory first to install it.  (Delete first so you can run the block more than once.)<br>\n!rm -rf /kaggle/working/asciitree-0.3.3<br>\n!cp -R /kaggle/input/zarr-dependencies-dataset/asciitree-0.3.3 /kaggle/working/.<br>\n!pip install --no-index /kaggle/working/asciitree-0.3.3/asciitree-0.3.3</p></li>\n<li><p>Then install zarr as described in the notebook above.<br>\n!pip install --no-index --find-links /kaggle/input/zarr-dependencies-dataset /kaggle/input/zarr-dependencies-dataset/zarr-2.18.3-py3-none-any.whl</p></li>\n<li><p>Import as normal.</p></li>\n</ol>\n<p>Hope this helps!</p>",
      "rawMarkdown": "Took me a bit to figure this out.  Aside from no internet access, the asciitree dependency is what makes this more difficult than usual.  Here were my steps:\n1. Create a dataset that includes the zarr dependencies as described in the following notebook.  Basically this involves calling \"!pip download zarr\" from a new notebook and making a dataset from the output.\n[https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet](https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet)\n\n2. Add the dataset to your notebook.  In step 4 below, I've named mine \"Zarr Dependencies Dataset\".\n\n3. Copy the asciitree directory to the working directory first to install it.  (Delete first so you can run the block more than once.)\n!rm -rf /kaggle/working/asciitree-0.3.3\n!cp -R /kaggle/input/zarr-dependencies-dataset/asciitree-0.3.3 /kaggle/working/.\n!pip install --no-index /kaggle/working/asciitree-0.3.3/asciitree-0.3.3\n\n4. Then install zarr as described in the notebook above.\n!pip install --no-index --find-links /kaggle/input/zarr-dependencies-dataset /kaggle/input/zarr-dependencies-dataset/zarr-2.18.3-py3-none-any.whl\n\n5. Import as normal.\n\nHope this helps!",
      "votes": null
    },
    {
      "id": "3040044",
      "postDate": "11/08/2024 16:17:14",
      "content": "<p>that is the old method.<br>\nthe new method is to use package manager</p>\n<p><a href=\"https://www.kaggle.com/discussions/product-feedback/532336\" target=\"_blank\">https://www.kaggle.com/discussions/product-feedback/532336</a></p>",
      "rawMarkdown": "that is the old method.\nthe new method is to use package manager\n\nhttps://www.kaggle.com/discussions/product-feedback/532336",
      "votes": null
    },
    {
      "id": "3040063",
      "postDate": "11/08/2024 16:39:02",
      "content": "<p>Thanks!  I will take a look.</p>",
      "rawMarkdown": "Thanks!  I will take a look.",
      "votes": null
    },
    {
      "id": "3040209",
      "postDate": "11/08/2024 21:07:44",
      "content": "<p>Yes, I also use the new Package Manager. Please note that there are some nuances to using that for submitting competitions. There is a workaround here: <a href=\"https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065\" target=\"_blank\">https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065</a></p>",
      "rawMarkdown": "Yes, I also use the new Package Manager. Please note that there are some nuances to using that for submitting competitions. There is a workaround here: https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065",
      "votes": null
    },
    {
      "id": "3040247",
      "postDate": "11/08/2024 22:02:53",
      "content": "<p><a href=\"https://www.kaggle.com/kharrington\" target=\"_blank\">@kharrington</a> Does the old way still work?</p>",
      "rawMarkdown": "kharrington Does the old way still work?",
      "votes": null
    },
    {
      "id": "3040969",
      "postDate": "11/09/2024 18:41:43",
      "content": "<p>Yes, the old way still works.</p>",
      "rawMarkdown": "Yes, the old way still works.",
      "votes": null
    },
    {
      "id": "3043492",
      "postDate": "11/12/2024 12:52:16",
      "content": "<p>Thanks!!　<br>\nThis was helpful because I didn't know how to install the package.</p>",
      "rawMarkdown": "Thanks!!　\nThis was helpful because I didn't know how to install the package.",
      "votes": null
    },
    {
      "id": "3091239",
      "postDate": "01/08/2025 07:51:39",
      "content": "<p>That works. Thank you very much</p>",
      "rawMarkdown": "That works. Thank you very much",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3040044,
      "author_name": "hengck23",
      "author_url": "",
      "post_date": "11/08/2024 16:17:14",
      "content": "<p>that is the old method.<br>\nthe new method is to use package manager</p>\n<p><a href=\"https://www.kaggle.com/discussions/product-feedback/532336\" target=\"_blank\">https://www.kaggle.com/discussions/product-feedback/532336</a></p>",
      "votes": null,
      "replies": [
        {
          "id": 3040063,
          "author_name": "davidlist",
          "author_url": "",
          "post_date": "11/08/2024 16:39:02",
          "content": "<p>Thanks!  I will take a look.</p>",
          "votes": null,
          "replies": [
            {
              "id": 3040209,
              "author_name": "kharrington",
              "author_url": "",
              "post_date": "11/08/2024 21:07:44",
              "content": "<p>Yes, I also use the new Package Manager. Please note that there are some nuances to using that for submitting competitions. There is a workaround here: <a href=\"https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065\" target=\"_blank\">https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065</a></p>",
              "votes": null,
              "replies": [
                {
                  "id": 3040247,
                  "author_name": "davidlist",
                  "author_url": "",
                  "post_date": "11/08/2024 22:02:53",
                  "content": "<p><a href=\"https://www.kaggle.com/kharrington\" target=\"_blank\">@kharrington</a> Does the old way still work?</p>",
                  "votes": null,
                  "replies": [
                    {
                      "id": 3040969,
                      "author_name": "coderrkj",
                      "author_url": "",
                      "post_date": "11/09/2024 18:41:43",
                      "content": "<p>Yes, the old way still works.</p>",
                      "votes": null,
                      "replies": []
                    }
                  ]
                }
              ]
            }
          ]
        },
        {
          "id": 3043492,
          "author_name": "ryoichiinoue",
          "author_url": "",
          "post_date": "11/12/2024 12:52:16",
          "content": "<p>Thanks!!　<br>\nThis was helpful because I didn't know how to install the package.</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 3091239,
      "author_name": "mingwangsong",
      "author_url": "",
      "post_date": "01/08/2025 07:51:39",
      "content": "<p>That works. Thank you very much</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3039379": "Took me a bit to figure this out.  Aside from no internet access, the asciitree dependency is what makes this more difficult than usual.  Here were my steps:\n1. Create a dataset that includes the zarr dependencies as described in the following notebook.  Basically this involves calling \"!pip download zarr\" from a new notebook and making a dataset from the output.\n[https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet](https://www.kaggle.com/code/panozzaj/installing-pip-packages-on-kaggle-without-internet)\n\n2. Add the dataset to your notebook.  In step 4 below, I've named mine \"Zarr Dependencies Dataset\".\n\n3. Copy the asciitree directory to the working directory first to install it.  (Delete first so you can run the block more than once.)\n!rm -rf /kaggle/working/asciitree-0.3.3\n!cp -R /kaggle/input/zarr-dependencies-dataset/asciitree-0.3.3 /kaggle/working/.\n!pip install --no-index /kaggle/working/asciitree-0.3.3/asciitree-0.3.3\n\n4. Then install zarr as described in the notebook above.\n!pip install --no-index --find-links /kaggle/input/zarr-dependencies-dataset /kaggle/input/zarr-dependencies-dataset/zarr-2.18.3-py3-none-any.whl\n\n5. Import as normal.\n\nHope this helps!",
    "3040044": "that is the old method.\nthe new method is to use package manager\n\nhttps://www.kaggle.com/discussions/product-feedback/532336",
    "3040063": "Thanks!  I will take a look.",
    "3040209": "Yes, I also use the new Package Manager. Please note that there are some nuances to using that for submitting competitions. There is a workaround here: https://www.kaggle.com/code/kharrington/blobdetector/comments#3039065",
    "3040247": "kharrington Does the old way still work?",
    "3040969": "Yes, the old way still works.",
    "3043492": "Thanks!!　\nThis was helpful because I didn't know how to install the package.",
    "3091239": "That works. Thank you very much"
  },
  "source": "meta"
}