updated env & tutorial1

bmandracchia · Oct 17, 2024 · 3467e89 · 3467e89
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diff --git a/bioMONAI/callbacks.py b/bioMONAI/callbacks.py
@@ -1,3 +1,5 @@
+"""Event handlers"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/07_callbacks.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/core.py b/bioMONAI/core.py
@@ -1,3 +1,5 @@
+"""bioMONAI core functions"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/00_core.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/data.py b/bioMONAI/data.py
@@ -1,3 +1,5 @@
+"""Data classes and functions"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/01_data.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/datasets.py b/bioMONAI/datasets.py
@@ -1,3 +1,5 @@
+"""Download and store datasets"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/08_datasets.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/io.py b/bioMONAI/io.py
@@ -1,3 +1,5 @@
+"""input/output management"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/02_io.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/losses.py b/bioMONAI/losses.py
@@ -1,3 +1,5 @@
+"""A set of custom loss functions"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_losses.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/metrics.py b/bioMONAI/metrics.py
@@ -1,3 +1,5 @@
+"""Metric tracking and analysis tools"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/06_metrics.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/nets.py b/bioMONAI/nets.py
@@ -1,3 +1,5 @@
+"""Neural networks"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/04_nets.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/transforms.py b/bioMONAI/transforms.py
@@ -1,3 +1,5 @@
+"""Data transformations and augmentations for 2D and 3D BioImages"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/05_transforms.ipynb.
 
 # %% auto 0

diff --git a/bioMONAI/visualize.py b/bioMONAI/visualize.py
@@ -1,3 +1,5 @@
+"""Data visualization"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/09_visualize.ipynb.
 
 # %% auto 0

diff --git a/biomonai.yml b/biomonai.yml
@@ -78,7 +78,6 @@ dependencies:
   - execnb=0.1.5=py_0
   - executing=0.8.3=pyhd3eb1b0_0
   - expat=2.5.0=h6a678d5_0
-  - fastcore=1.5.29=py_0
   - fastdownload=0.0.7=py_0
   - fastprogress=1.0.3=py_0
   - ffmpeg=4.3=hf484d3e_0
@@ -205,7 +204,6 @@ dependencies:
   - munkres=1.1.4=py_0
   - murmurhash=1.0.7=py311h6a678d5_0
   - mysql=5.7.24=h721c034_2
-  - nbdev=2.3.13=py_0
   - ncurses=6.4=h6a678d5_0
   - nest-asyncio=1.5.6=py311h06a4308_0
   - nettle=3.7.3=hbbd107a_1
@@ -324,14 +322,17 @@ dependencies:
       - distro==1.8.0
       - einops==0.8.0
       - elementpath==4.4.0
-      - fastai==2.7.12
+      - fastai==2.7.17
       - fastapi==0.105.0
+      - fastcore==1.7.17
       - fasteners==0.19
       - fastjsonschema==2.20.0
       - ffmpy==0.3.1
+      - fire==0.6.0
       - frozenlist==1.4.1
       - fsspec==2023.6.0
       - gdown==4.7.1
+      - ghp-import==2.1.0
       - gradio==4.9.0
       - gradio-client==0.7.2
       - h11==0.14.0
@@ -356,10 +357,12 @@ dependencies:
       - locket==1.0.0
       - lxml==4.9.4
       - mamba-ssm==2.2.2
+      - medmnist==3.0.2
       - monai==1.3.2
       - msgpack==1.0.8
       - multidict==6.0.5
       - multipagetiff==3.0.9
+      - nbdev==2.3.31
       - nbformat==5.10.4
       - nibabel==5.2.0
       - ninja==1.11.1.1
@@ -414,6 +417,7 @@ dependencies:
       - starlette==0.27.0
       - tblib==3.0.0
       - tenacity==8.2.3
+      - termcolor==2.4.0
       - thinc==8.2.1
       - tifffile==2023.2.28
       - tokenizers==0.19.1
@@ -435,4 +439,4 @@ dependencies:
       - zarr==2.15.0
       - zict==3.0.0
       - zipp==3.17.0
-prefix: /home/biagio/miniconda3/envs/bioMONAI-env
+prefix: /home/biagio/miniconda3/envs/bioMONAI-env
diff --git a/biomonai2.yml b/biomonai2.yml