One-stop-shop Mamba/Conda alternative to Python venv

.gitattributes

@@ -0,0 +1,2 @@
+masks/*.nii filter=lfs diff=lfs merge=lfs -text
+trained_models/*.models filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -204,4 +204,4 @@ Thumbs.db
 .history
 .ionide
 
-# End of https://www.toptal.com/developers/gitignore/api/macos,linux,python,visualstudiocode
+# End of https://www.toptal.com/developers/gitignore/api/macos,linux,python,visualstudiocode

.lfsconfig

@@ -0,0 +1,2 @@
+[lfs]
+	url = https://AInII@dev.azure.com/AInII/brainage_estimation/_git/brainage_estimation.git/info/lfs

README.md

@@ -12,6 +12,14 @@ pip install https://github.com/JamesRitchie/scikit-rvm/archive/master.zip
 pip install glmnet
 ```
 
+Alternatively, you may use Mamba to create an environment including all of the above:
+```
+$ git clone https://github.com/juaml/brainage_estimation.git
+$ cd brainage_estimation
+$ mamba env create --file requirements.yml
+$ mamba activate brainage_estimation
+```
+
 After the set up following codes can be run as provided in the `codes` directory.
 
 2. **Get predictions** 

codes/predict_age.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 #from read_data_mask_resampled import *
 from brainage import calculate_voxelwise_features
 from pathlib import Path

requirements.yml

@@ -0,0 +1,63 @@
+name: brainage_estimation
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - Python==3.9.1
+  - pip==23.3.1
+  - asttokens==2.0.5
+  - backcall==0.2.0
+  - certifi==2021.10.8
+  - charset-normalizer==2.0.12
+  - commonmark==0.9.1
+  - convertdate==2.4.0
+  - cycler==0.11.0
+  - decorator==5.1.1
+  - executing==0.8.3
+  - fonttools==4.31.2
+  - numpy==1.22.3
+  - idna==3.3
+  - ipython==8.2.0
+  - jedi==0.18.1
+  - joblib==1.1.0
+  - kiwisolver==1.4.2
+  - lunardate==0.2.0
+  - lxml==4.8.0
+  - matplotlib==3.5.1
+  - matplotlib-inline==0.1.3
+  - natsort==8.1.0
+  - nibabel==3.2.2
+  - nilearn==0.9.1
+  - packaging==21.3
+  - pandas==1.4.2
+  - parso==0.8.3
+  - pexpect==4.8.0
+  - pickleshare==0.7.5
+  - Pillow==9.1.0
+  - prompt-toolkit==3.0.29
+  - ptyprocess==0.7.0
+  - pure_eval==0.2.2
+  - Pygments==2.11.2
+  - pyluach==1.4.1
+  - pyparsing==3.0.7
+  - python-dateutil==2.8.2
+  - pytz==2022.1
+  - requests==2.27.1
+  - rich==12.2.0
+  - scikit-learn==1.0.2
+  - scipy==1.8.0
+  - seaborn==0.11.2
+  - six==1.16.0
+  - stack_data==0.2.0
+  - threadpoolctl==3.1.0
+  - traitlets==5.1.1
+  - urllib3==1.26.9
+  - wcwidth==0.2.5
+  - workalendar==16.3.0
+  - glmnet==2.2.1
+  - pip:
+    - julearn==0.2.5
+    - PyMeeus==0.5.11
+    - xgboost==1.6.0
+    - https://github.com/JamesRitchie/scikit-rvm/archive/b5b5f0a062b877f9cbaae219113a7e7b5a19b881.zip
+    - .