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Merged
merged 1 commit into from
Dec 13, 2021
Merged

Remove developer names/aliases from notebooks and documentation #225

merged 1 commit into from
Dec 13, 2021

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KavinKrishnan
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whoisj
whoisj requested changes Dec 8, 2021
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ideally we had a standardized path we use in these examples so that if a user followed the example verbatim everything just worked.

to that end, I recommend we use ~/src/monai-deploy-app-sdk/ as the working folder.

notebooks/tutorials/04_mis_tutorial.ipynb
@@ -162,7 +162,7 @@
"remote: Total 274 (delta 127), reused 213 (delta 90), pack-reused 0\u001b[K\n",
"Receiving objects: 100% (274/274), 79.20 KiB | 705.00 KiB/s, done.\n",
"Resolving deltas: 100% (127/127), done.\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
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can we replace /home/<user> with ~ ?

notebooks/tutorials/04_mis_tutorial.ipynb
@@ -201,7 +201,7 @@
" ---> a6834eb5a23b\n",
"Successfully built a6834eb5a23b\n",
"Successfully tagged monai/inference-service:0.1\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials\n"
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can we replace /home/ with ~ ?

notebooks/tutorials/04_mis_tutorial.ipynb
@@ -230,7 +230,7 @@
"text": [
"Downloading...\n",
"From: https://drive.google.com/uc?id=12uNO1tyqZh1oFkZH41Osliey7TRm-BBG\n",
"To: /home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
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can we replace /home/ with ~ ?

notebooks/tutorials/04_mis_tutorial.ipynb
@@ -453,7 +453,7 @@
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gupta/miniconda3/envs/monairsna/lib/python3.6/site-packages (from requests[socks]->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /data/Vikash/Tools/RSNA/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
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we should standardize this path so that it copy/pasted it just works.

notebooks/tutorials/05_full_tutorial.ipynb
@@ -129,7 +129,7 @@
"Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/gbae/miniconda3/envs/mednist/lib/python3.6/site-packages (from requests[socks]>=2.12.0->gdown) (1.7.1)\n",
"Downloading...\n",
"From: https://drive.google.com/uc?id=1GC_N8YQk_mOWN02oOzAU_2YDmNRWk--n\n",
"To: /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_data_updated_1203.zip\n",
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can we replace /home/<user> with ~ ?

we should also standardize the path we use. I recommend using ~/src/monai-deploy-app-sdk/.

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~/src/ only works if that directory is created in advance.

We can also use a variable the repopath, eg: export MONAIREPO=${PWD}

notebooks/tutorials/05_full_tutorial.ipynb
@@ -1320,7 +1320,7 @@
"[2021-09-23 02:20:44,984] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Number of slices in the numpy image: 515\n",
"[2021-09-23 02:20:44,984] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Labels of the segments: ['Spleen']\n",
"[2021-09-23 02:20:47,101] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Unique values in seg image: [0 1]\n",
"[2021-09-23 02:20:48,312] [INFO] (monai.deploy.operators.dicom_seg_writer_operator.DICOMSegWriter) - Saving output file /home/gbae/repo/monai-deploy-app-sdk/notebooks/tutorials/output/dicom_seg-DICOMSEG.dcm\n",
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can we replace /home/<user> with ~ ?

notebooks/tutorials/05_full_tutorial.ipynb
@@ -1683,7 +1683,7 @@
"remote: Total 274 (delta 127), reused 213 (delta 90), pack-reused 0\u001b[K\n",
"Receiving objects: 100% (274/274), 79.20 KiB | 705.00 KiB/s, done.\n",
"Resolving deltas: 100% (127/127), done.\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/monai-deploy-app-server/components/inference-service\n",
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can we replace /home/<user> with ~ ?

notebooks/tutorials/05_full_tutorial.ipynb
@@ -1722,7 +1722,7 @@
" ---> a6834eb5a23b\n",
"Successfully built a6834eb5a23b\n",
"Successfully tagged monai/inference-service:0.1\n",
"/home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials\n"
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can we replace /home/<user> with ~ ?

notebooks/tutorials/05_full_tutorial.ipynb
@@ -1751,7 +1751,7 @@
"text": [
"Downloading...\n",
"From: https://drive.google.com/uc?id=12uNO1tyqZh1oFkZH41Osliey7TRm-BBG\n",
"To: /home/kavink/src/work_folder/monai-deploy-app-sdk/notebooks/tutorials/charts.zip\n",
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can we replace /home/<user> with ~ ?

notebooks/tutorials/05_full_tutorial.ipynb
@@ -2042,7 +2042,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/home/kavink/.local/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.\n",
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can we replace /home/<user> with ~ ?

@whoisj whoisj added bug Something isn't working documentation Improvements or additions to documentation labels Dec 8, 2021
@KavinKrishnan KavinKrishnan force-pushed the kavink/cleanup_notebooks_w_names branch from 37aa882 to 1f6d6a5 Compare December 13, 2021 19:36
gigony
gigony approved these changes Dec 13, 2021
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Looks good to me.

You can use home/<user> with /home/monai/. Either way (~) is fine.

@KavinKrishnan KavinKrishnan force-pushed the kavink/cleanup_notebooks_w_names branch 2 times, most recently from 5f1aaab to d768579 Compare December 13, 2021 21:16
@KavinKrishnan KavinKrishnan merged commit 0aa7ef0 into main Dec 13, 2021
@KavinKrishnan
Remove developer names/aliases from notebooks and documentation
d768579 
Signed-off-by: kavink <kavink@nvidia.com>
@gigony gigony mentioned this pull request Jan 25, 2022
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@evberrypi evberrypi evberrypi left review comments

@whoisj whoisj whoisj requested changes

@gigony gigony gigony approved these changes

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@KavinKrishnan @gigony @whoisj @evberrypi