Merging recent changes into main

.github/workflows/code-quality-main.yaml

@@ -13,10 +13,10 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
 
       - name: Run pre-commits
-        uses: pre-commit/action@v2.0.3
+        uses: pre-commit/action@v3.0.0

.github/workflows/code-quality-pr.yaml

@@ -16,10 +16,10 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
 
       - name: Find modified files
         id: file_changes
@@ -31,6 +31,6 @@ jobs:
         run: echo '${{ steps.file_changes.outputs.files}}'
 
       - name: Run pre-commits
-        uses: pre-commit/action@v2.0.3
+        uses: pre-commit/action@v3.0.0
         with:
           extra_args: --files ${{ steps.file_changes.outputs.files}}

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
 
-    timeout-minutes: 20
+    timeout-minutes: 30
 
     steps:
       - name: Checkout
@@ -24,48 +24,20 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Add conda to system path
+      - name: Install packages
         run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install dependencies
-        run: |
-          conda env update --file env_cpu.yml --name base
-          pip install pytest
-          pip install sh
-
-      - name: List dependencies
-        run: |
-          conda list
-
-      - name: Run pytest
-        run: |
-          pytest -v --doctest-modules --ignore docs/
-
-  # upload code coverage report
-  code-coverage:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.10"
-
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install dependencies
-        run: |
-          conda env update --file env_cpu.yml --name base
+          pip install -e .
           pip install pytest
           pip install pytest-cov[toml]
-          pip install sh
+          pip install nbmake
+          pip install rootutils
 
-      - name: Run tests and collect coverage
-        run: pytest --doctest-modules --cov EventStream --ignore docs/
+      #----------------------------------------------
+      #              run test suite
+      #----------------------------------------------
+      - name: Run tests
+        run: |
+          pytest -v --doctest-modules --cov EventStream --ignore docs/ --nbmake
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

.gitignore

@@ -140,3 +140,8 @@ logfile
 tags
 
 docs/_collections/*
+docs/bin
+
+sample_data/processed/*
+
+outputs

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 default_language_version:
   python: python3
 
-exclude: "sample_data"
+exclude: "sample_data|docs/MIMIC_IV_tutorial/wandb_reports"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -19,11 +19,10 @@ repos:
       - id: check-case-conflict
       - id: check-added-large-files
         args: [--maxkb, "800"]
-        exclude: "sample_data"
 
   # python code formatting
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.7.0
     hooks:
       - id: black
         args: [--line-length, "110"]
@@ -33,30 +32,30 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
-        args: ["--profile", "black", "--filter-files"]
+        args: ["--profile", "black", "--filter-files", "-o", "wandb"]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.1.1
+    rev: v2.2.0
     hooks:
       - id: autoflake
 
   # python upgrading syntax to newer version
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.10.1
     hooks:
       - id: pyupgrade
         args: [--py310-plus]
 
   # python docstring formatting
   - repo: https://github.com/myint/docformatter
-    rev: v1.5.1
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]
 
   # python check (PEP8), programming errors and code complexity
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         args:
@@ -73,21 +72,21 @@ repos:
 
   # yaml formatting
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+    rev: v3.0.3
     hooks:
       - id: prettier
         types: [yaml]
         exclude: "environment.yaml"
 
   # shell scripts linter
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.9.0.2
+    rev: v0.9.0.5
     hooks:
       - id: shellcheck
 
   # md formatting
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         args: ["--number"]
@@ -102,11 +101,11 @@ repos:
 
   # word spelling linter
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
       - id: codespell
         args:
-          - --skip=logs/**,data/**,*.ipynb,*.bib,env.yml,env_cpu.yml,*.svg
+          - --skip=logs/**,data/**,*.ipynb,*.bib,env.yml,env_cpu.yml,*.svg,poetry.lock
           - --ignore-words-list=ehr
 
   # jupyter notebook cell output clearing
@@ -117,7 +116,7 @@ repos:
 
   # jupyter notebook linting
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.3
+    rev: 1.7.0
     hooks:
       - id: nbqa-black
         args: ["--line-length=110"]

.readthedocs.yaml

@@ -8,15 +8,18 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
+    python: "3.10"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-
 # Optionally build your docs in additional formats such as PDF
 # formats:
 #  - pdf
-
-conda:
-  environment: env_cpu.yml