adding deps reconstruction notebook (#17)

Co-authored-by: Laksh <laksh.arumugam@recursionpharma.com>

requirements.in

@@ -9,6 +9,9 @@ xformers
 zarr
 hydra-core
 pytorch-lightning>=2.1
+matplotlib
+scikit-image
+ipykernel
 isort
 ruff
 pytest

requirements.txt

@@ -18,6 +18,8 @@ antlr4-python3-runtime==4.9.3
     #   omegaconf
 asciitree==0.3.3
     # via zarr
+asttokens==2.4.1
+    # via stack-data
 async-timeout==4.0.3
     # via aiohttp
 attrs==24.2.0
@@ -26,8 +28,22 @@ certifi==2024.8.30
     # via requests
 charset-normalizer==3.4.0
     # via requests
+comm==0.2.2
+    # via ipykernel
+contourpy==1.3.0
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+debugpy==1.8.7
+    # via ipykernel
+decorator==5.1.1
+    # via ipython
 exceptiongroup==1.2.2
-    # via pytest
+    # via
+    #   ipython
+    #   pytest
+executing==2.1.0
+    # via stack-data
 fasteners==0.19
     # via zarr
 filelock==3.16.1
@@ -36,7 +52,9 @@ filelock==3.16.1
     #   torch
     #   transformers
     #   triton
-frozenlist==1.4.1
+fonttools==4.54.1
+    # via matplotlib
+frozenlist==1.5.0
     # via
     #   aiohttp
     #   aiosignal
@@ -45,7 +63,7 @@ fsspec[http]==2024.10.0
     #   huggingface-hub
     #   pytorch-lightning
     #   torch
-huggingface-hub==0.26.1
+huggingface-hub==0.26.2
     # via
     #   -r requirements.in
     #   timm
@@ -57,31 +75,65 @@ idna==3.10
     # via
     #   requests
     #   yarl
+imageio==2.36.0
+    # via scikit-image
 iniconfig==2.0.0
     # via pytest
+ipykernel==6.29.5
+    # via -r requirements.in
+ipython==8.29.0
+    # via ipykernel
 isort==5.13.2
     # via -r requirements.in
+jedi==0.19.1
+    # via ipython
 jinja2==3.1.4
     # via torch
+jupyter-client==8.6.3
+    # via ipykernel
+jupyter-core==5.7.2
+    # via
+    #   ipykernel
+    #   jupyter-client
+kiwisolver==1.4.7
+    # via matplotlib
+lazy-loader==0.4
+    # via scikit-image
 lightning-utilities==0.11.8
     # via
     #   pytorch-lightning
     #   torchmetrics
 markupsafe==3.0.2
     # via jinja2
+matplotlib==3.9.2
+    # via -r requirements.in
+matplotlib-inline==0.1.7
+    # via
+    #   ipykernel
+    #   ipython
 mpmath==1.3.0
     # via sympy
 multidict==6.1.0
     # via
     #   aiohttp
     #   yarl
-networkx==3.4.2
-    # via torch
-numcodecs==0.13.1
+nest-asyncio==1.6.0
+    # via ipykernel
+networkx==3.2.1
+    # via
+    #   scikit-image
+    #   torch
+numcodecs==0.12.1
     # via zarr
 numpy==1.26.4
     # via
+    #   contourpy
+    #   imageio
+    #   matplotlib
     #   numcodecs
+    #   scikit-image
+    #   scipy
+    #   tifffile
     #   torchmetrics
     #   torchvision
     #   transformers
@@ -125,19 +177,49 @@ packaging==24.1
     # via
     #   huggingface-hub
     #   hydra-core
+    #   ipykernel
+    #   lazy-loader
     #   lightning-utilities
+    #   matplotlib
     #   pytest
     #   pytorch-lightning
+    #   scikit-image
     #   torchmetrics
     #   transformers
+parso==0.8.4
+    # via jedi
+pexpect==4.9.0
+    # via ipython
 pillow==11.0.0
-    # via torchvision
+    # via
+    #   imageio
+    #   matplotlib
+    #   scikit-image
+    #   torchvision
+platformdirs==4.3.6
+    # via jupyter-core
 pluggy==1.5.0
     # via pytest
+prompt-toolkit==3.0.48
+    # via ipython
 propcache==0.2.0
     # via yarl
+psutil==6.1.0
+    # via ipykernel
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pygments==2.18.0
+    # via ipython
+pyparsing==3.2.0
+    # via matplotlib
 pytest==8.3.3
     # via -r requirements.in
+python-dateutil==2.9.0.post0
+    # via
+    #   jupyter-client
+    #   matplotlib
 pytorch-lightning==2.4.0
     # via -r requirements.in
 pyyaml==6.0.2
@@ -147,27 +229,43 @@ pyyaml==6.0.2
     #   pytorch-lightning
     #   timm
     #   transformers
+pyzmq==26.2.0
+    # via
+    #   ipykernel
+    #   jupyter-client
 regex==2024.9.11
     # via transformers
 requests==2.32.3
     # via
     #   huggingface-hub
     #   transformers
-ruff==0.7.0
+ruff==0.7.2
     # via -r requirements.in
 safetensors==0.4.5
     # via
     #   timm
     #   transformers
+scikit-image==0.24.0
+    # via -r requirements.in
+scipy==1.13.1
+    # via scikit-image
+six==1.16.0
+    # via
+    #   asttokens
+    #   python-dateutil
+stack-data==0.6.3
+    # via ipython
 sympy==1.13.1
     # via torch
+tifffile==2024.8.30
+    # via scikit-image
 timm==1.0.11
     # via -r requirements.in
-tokenizers==0.20.1
+tokenizers==0.20.2
     # via transformers
 tomli==2.0.2
     # via pytest
-torch==2.5.0
+torch==2.5.1
     # via
     #   -r requirements.in
     #   pytorch-lightning
@@ -175,38 +273,53 @@ torch==2.5.0
     #   torchmetrics
     #   torchvision
     #   xformers
-torchmetrics==1.5.0
+torchmetrics==1.5.1
     # via
     #   -r requirements.in
     #   pytorch-lightning
-torchvision==0.20.0
+torchvision==0.20.1
     # via
     #   -r requirements.in
     #   timm
-tqdm==4.66.5
+tornado==6.4.1
+    # via
+    #   ipykernel
+    #   jupyter-client
+tqdm==4.66.6
     # via
     #   -r requirements.in
     #   huggingface-hub
     #   pytorch-lightning
     #   transformers
-transformers==4.45.2
+traitlets==5.14.3
+    # via
+    #   comm
+    #   ipykernel
+    #   ipython
+    #   jupyter-client
+    #   jupyter-core
+    #   matplotlib-inline
+transformers==4.46.1
     # via -r requirements.in
 triton==3.1.0
     # via torch
 typing-extensions==4.12.2
     # via
     #   huggingface-hub
+    #   ipython
     #   lightning-utilities
     #   multidict
     #   pytorch-lightning
     #   torch
 urllib3==2.2.3
     # via requests
-xformers==0.0.28.post2
+wcwidth==0.2.13
+    # via prompt-toolkit
+xformers==0.0.28.post3
     # via -r requirements.in
-yarl==1.16.0
+yarl==1.17.1
     # via aiohttp
-zarr==2.18.3
+zarr==2.18.2
     # via -r requirements.in
 
 # The following packages are considered to be unsafe in a requirements file: