Improve test coverage and documentation (#64)

* Add visualize_benchmark function * Improve test coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage, add is_fitted checks * Update BaseEstimator validator * Continue improving coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage * Continue improving coverage * Improve coverage - serialization * Continue improving coverage - models/ddh * Continue improving coverage - models * Continue improving coverage - models/ts_model * Continue improving coverage - models * Update AUTHORS * Add tutorials -> docs user guide conversion * Update README examples * Update image * Reorganize README * Update README * Update README * Update README * Update image * Add dev docs * Add favicon, workaround for logo * Remove xdist from test_*.yml * Fix previous commit * Remove keepalive action * Restore xdist * Add multiple dependency versions test workflow * Update test_deps * Tidy README * CI failure investigation: Try no para. & no vis * Restore xdist, keep vis. test disabled * Previous commit continued
vanderschaarlab · May 30, 2023 · 67ebd74 · 67ebd74
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commit 67ebd74
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -47,9 +47,6 @@ jobs:
  - uses: actions/checkout@v3
  with:
  submodules: true
- # Prevents scheduled run being disabled after no commit
- # for some time (creates a dummy commit):
- - uses: gautamkrishnar/keepalive-workflow@v1
  - name: Set up Python ${{ matrix.python-version }}
  uses: actions/setup-python@v4
  with:

diff --git a/.github/workflows/test_deps.yml b/.github/workflows/test_deps.yml
@@ -0,0 +1,70 @@
+name: "Tests: Dependency Versions"
+
+on:
+ schedule:
+ # This schedule is monthly.
+ - cron: "29 3 12 * *"
+ workflow_dispatch:
+
+jobs:
+ # Lint code with pre-commit.
+ Linter:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ python-version: [3.8]
+ os: [ubuntu-latest]
+ env:
+ CODECOV_OS: ${{ matrix.os }}
+ CODECOV_PYTHON: ${{ matrix.python-version }}
+ steps:
+ - uses: actions/checkout@v3
+ with:
+ submodules: true
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ pip install --upgrade pip
+ pip install pre-commit
+ - name: Run pre-commit validation
+ run: pre-commit run --all-files
+
+ # Run tests with pytest.
+ # Test with the dependency versions specified in the matrix.
+ Tests:
+ needs: [Linter]
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ python-version: [3.8]
+ os: [ubuntu-latest]
+ dep:
+ - torch==1.10
+ - torch>=2
+ - pandas==1.3
+ - pandas>=2
+ - numpy==1.20
+ - numpy>=1.24
+ steps:
+ - uses: actions/checkout@v3
+ with:
+ submodules: true
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ cache: "pip" # Caching pip dependencies.
+ - name: Install dependencies
+ run: |
+ pip install --upgrade pip
+ pip install .[dev]
+ pip install "${{ matrix.python-version }}"
+ - name: Test with pytest (xdist)
+ if: matrix.os != 'ubuntu-latest'
+ run: pytest -vvvx -n auto -m "not slow and not extra and not skipci" --durations=50 --cov
+ - name: Test with pytest
+ if: matrix.os == 'ubuntu-latest'
+ run: pytest -vvvx -m "not slow and not extra and not skipci" --durations=50 --cov
diff --git a/.github/workflows/test_full.yml b/.github/workflows/test_full.yml
@@ -43,9 +43,6 @@ jobs:
  - uses: actions/checkout@v3
  with:
  submodules: true
- # Prevents scheduled run being disabled after no commit
- # for some time (creates a dummy commit):
- - uses: gautamkrishnar/keepalive-workflow@v1
  - name: Set up Python ${{ matrix.python-version }}
  uses: actions/setup-python@v4
  with:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,6 +6,7 @@ repos:
  hooks:
  - id: trailing-whitespace
  args: ['--markdown-linebreak-ext=md']
+ exclude: 'docs/user_guide' # Auto-generated, leave as is.
  - id: check-added-large-files
  args: ['--maxkb=1000']
  - id: check-ast
@@ -18,6 +19,7 @@ repos:
  - id: check-executables-have-shebangs
  - id: debug-statements
  - id: end-of-file-fixer
+ exclude: 'docs/user_guide' # Auto-generated, leave as is.
  - id: pretty-format-json
  args: ['--autofix', '--indent=4', '--no-sort-keys']
  - id: requirements-txt-fixer
@@ -45,6 +47,7 @@ repos:
  hooks:
  - id: blacken-docs
  additional_dependencies: [black]
+ exclude: 'docs/user_guide' # Auto-generated, leave as is.
 
 - repo: https://github.com/PyCQA/flake8
  rev: 6.0.0

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -15,8 +15,8 @@ sphinx:
  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF
-# formats:
-#  - pdf
+formats:
+ - pdf
 
 python:
  install:

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -1,3 +1,4 @@
 # Contributors
 
 * Evgeny Saveliev [[email protected]](mailto:[email protected])
+* Bogdan Cebere [[email protected]](mailto:[email protected])