Merge PR #1 from vanderschaarlab/main

Updates

.github/workflows/test_tutorials.yml

@@ -0,0 +1,39 @@
+name: PR Tutorials
+
+on:
+  push:
+    branches: [main, release]
+  pull_request:
+    types: [opened, synchronize, reopened]
+  schedule:
+    - cron: "2 3 * * 1"
+  workflow_dispatch:
+
+jobs:
+  Tutorials:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+      - uses: gautamkrishnar/keepalive-workflow@v1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip" # caching pip dependencies
+      - name: Install MacOS dependencies
+        run: |
+          brew install libomp
+        if: ${{ matrix.os == 'macos-latest' }}
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          pip install -r requirements.txt
+
+      - name: Run the tutorials
+        run: python tutorials/nb_eval.py --nb_dir tutorials/

.gitignore

@@ -162,4 +162,11 @@ cython_debug/
 # specific
 /data_all
 
-.DS_Store
+.DS_Store
+
+# Project specific
+data/*
+!data/Data-Private.md
+!data/Data-Public.md
+
+use_cases/checkpoint.pt

.pre-commit-config.yaml

@@ -1,33 +1,44 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.2.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: debug-statements
-    -   id: name-tests-test
-    -   id: requirements-txt-fixer
--   repo: https://github.com/asottile/setup-cfg-fmt
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: name-tests-test
+      - id: mixed-line-ending
+        args: ["--fix=auto"] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+  - repo: https://github.com/asottile/setup-cfg-fmt
     rev: v1.20.1
     hooks:
-    -   id: setup-cfg-fmt
--   repo: https://github.com/janosh/format-ipy-cells
+      - id: setup-cfg-fmt
+  - repo: https://github.com/janosh/format-ipy-cells
     rev: v0.1.10
     hooks:
       - id: format-ipy-cells
-- repo: http://github.com/timothycrosley/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    args: ["--profile", "black", "--filter-files"]
+  - repo: http://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
 
-- repo: https://github.com/psf/black
-  rev: 22.3.0
-  hooks:
-  - id: black
--   repo: https://github.com/asottile/add-trailing-comma
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/add-trailing-comma
     rev: v2.2.3
     hooks:
-    -   id: add-trailing-comma
-        args: [--py36-plus]
+      - id: add-trailing-comma
+        args: [--py36-plus]
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: ["--max-line-length=480", "--extend-ignore=E203,W503"]

AUTHORS.rst

@@ -0,0 +1,5 @@
+============
+Contributors
+============
+
+* Nabeel Seedat <seedatnabeel@gmail.com>

CHANGELOG.rst

@@ -0,0 +1,8 @@
+=========
+Changelog
+=========
+
+Version 0.1
+===========
+
+- Initial Version

data/Data-Public.md

@@ -4,4 +4,4 @@ All data should be placed in the ``\data`` folder
 
 ## Public
 
-* Public datasets can be found at the following link: https://drive.google.com/drive/folders/1iy-9UelW0CAA5XKxomAMaoEJE3Kbyn3q
+* Public datasets can be found at the following link: https://drive.google.com/drive/folders/1iy-9UelW0CAA5XKxomAMaoEJE3Kbyn3q

isort.cfg

@@ -5,4 +5,4 @@ line_length=88
 multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0
-use_parentheses=True
+use_parentheses=True

requirements-min.txt

@@ -1,10 +1,10 @@
 crepes==0.1.0
+ipykernel
+matplotlib
 numpy
-torch
-scikit-learn==1.3.0
-pandas==2.0.3
 openml==0.14.0
+pandas==2.0.3
+scikit-learn==1.3.0
+torch
+tqdm
 xgboost==1.7.6
-ipykernel
-matplotlib
-tqdm

requirements.txt

@@ -1,23 +1,22 @@
 autograd-lib
+black
 catboost==1.1
-xlrd
-opentsne
 crepes==0.1.0
-numpy
-torch
-scikit-learn==1.3.0
-pandas==2.0.3
-openml==0.14.0
-xgboost==1.7.6
-torch==1.13.1
-sdv==0.17.2
-xgboost==1.7.6
-SciencePlots==1.0.9
-hyperimpute==0.1.17
-black
-isort
 fairlearn==0.9.0
+hyperimpute==0.1.17
 ipykernel
+isort
 matplotlib==3.7.2
 ngboost==0.4.1
-pre-commit
+numpy
+openml==0.14.0
+opentsne
+pandas==1.5.3
+pre-commit
+SciencePlots==1.0.9
+scikit-learn==1.3.0
+sdv==0.17.2
+torch==1.13.1
+xgboost==1.7.6
+xgboost==1.7.6
+xlrd

setup.py

@@ -1,14 +1,15 @@
-from setuptools import setup
 import io
 import os
 import re
 
+from setuptools import setup
+
 here = os.path.realpath(os.path.dirname(__file__))
 
-name = 'TRIAGE'
+name = "TRIAGE"
 
 # for simplicity we actually store the version in the __version__ attribute in the source
-with io.open(os.path.join(here, name, '__init__.py')) as f:
+with io.open(os.path.join(here, name, "__init__.py")) as f:
     meta_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", f.read(), re.M)
     if meta_match:
         version = meta_match.group(1)
@@ -26,6 +27,6 @@
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "
             "setuptools_scm and wheel with:\n"
-            "   pip install -U setuptools setuptools_scm wheel\n\n"
+            "   pip install -U setuptools setuptools_scm wheel\n\n",
         )
-        raise
+        raise