Remove query package to port as a new tool (#495)

* Remove query package to port as a new tool

* Fix package install test checks

* Fix package install check workflow

* Create optional docs,test dependency groups, install cycquery under test

* Fix broken notebooks

.github/workflows/code_checks.yml

@@ -37,5 +37,5 @@ jobs:
         run: |
           poetry env use '3.10'
           source $(poetry env info --path)/bin/activate
-          poetry install --without dev,docs
+          poetry install --with test
           pre-commit run --all-files

.github/workflows/docs_build.yml

@@ -33,8 +33,7 @@ jobs:
           python3 -m pip install --upgrade pip && python3 -m pip install poetry
           poetry env use '3.10'
           source $(poetry env info --path)/bin/activate
-          poetry install --without dev
-          python3 -m ipykernel install --user --name cyclops
+          poetry install --with docs,test
           # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst
           cd docs && rm -rf source/reference/api/_autosummary && make html
           cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m

.github/workflows/docs_deploy.yml

@@ -35,8 +35,7 @@ jobs:
       - run: |
           poetry env use '3.10'
           source $(poetry env info --path)/bin/activate
-          poetry install --without dev
-          python3 -m ipykernel install --user --name cyclops
+          poetry install --with docs,test
           # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst
           cd docs && rm -rf source/reference/api/_autosummary && make html
           cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m

.github/workflows/integration_tests.yml

@@ -48,7 +48,7 @@ jobs:
         run: |
           poetry env use '3.10'
           source $(poetry env info --path)/bin/activate
-          poetry install --without dev,docs
+          poetry install --with test
           coverage run -m pytest -m integration_test && coverage xml && coverage report -m
       - name: Upload coverage to Codecov
         uses: Wandalen/wretry.action@v1.0.36

.github/workflows/package.yml

@@ -37,20 +37,6 @@ jobs:
           pip install -e .
           pip install pytest
           python3 -m pytest tests/package/*.py
-  extra-query-package-install-check:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install pip
-        run: python3 -m pip install --upgrade pip
-      - uses: actions/setup-python@v4.7.1
-        with:
-          python-version: '3.10'
-      - name: Install package and test import
-        run: |
-          pip install -e ".[query]"
-          pip install pytest
-          python3 -m pytest tests/package/extras/query.py
   extra-models-package-install-check:
     runs-on: ubuntu-latest
     steps:

.gitignore

@@ -28,3 +28,4 @@ multirun/
 _autosummary
 *cyclops_reports*
 *dummy_reports*
+.mypy_cache

.pre-commit-config.yaml

@@ -28,7 +28,7 @@ repos:
       types_or: [python, jupyter]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.1
     hooks:
     - id: mypy
       entry: python3 -m mypy --config-file pyproject.toml

README.md

@@ -12,7 +12,6 @@
 
 ``cyclops`` is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely:
 
-* `query` - Query EHR databases (such as MIMIC-IV)
 * `data` - Create datasets for training, inference and evaluation. We use the popular 🤗 [datasets](https://github.com/huggingface/datasets) to efficiently load and slice different modalities of data.
 * `models` - Use common model implementations using [scikit-learn](https://scikit-learn.org/stable/) and [PyTorch](https://pytorch.org/).
 * `tasks` - Use canonical Healthcare ML tasks such as
@@ -42,11 +41,6 @@ and transform clinical data, for downstream tasks.
 
 To install additional functionality from the other APIs, they can be installed as extras.
 
-To install with `query` API support,
-
-```bash
-python3 -m pip install 'pycyclops[query]'
-```
 
 To install with `models`, `tasks`, `evaluate` and `monitor` API support,
 
@@ -60,11 +54,11 @@ To install with `report` API support,
 python3 -m pip install 'pycyclops[report]'
 ```
 
-Multiple extras could also be combined, for example to install with both `query` and
+Multiple extras could also be combined, for example to install with both `report` and
 `models` support:
 
 ```bash
-python3 -m pip install 'pycyclops[query,models]'
+python3 -m pip install 'pycyclops[report,models]'
 ```
 
 
@@ -81,22 +75,17 @@ python3 -m poetry install
 source $(poetry env info --path)/bin/activate
 ```
 
-### Using Conda
-
-The development environment can also be set up using
-[conda](https://docs.conda.io/en/latest/). Hence, make sure it is
-installed and then run:
+In order to install dependencies for testing, run:
 
 ```bash
-conda env create
-conda install conda-build
-conda develop .
+python3 -m poetry install --with test
 ```
 
 API documentation is built using [Sphinx](https://www.sphinx-doc.org/en/master/) and
 can be locally built by:
 
 ```bash
+python3 -m poetry install --with docs
 cd docs
 make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
 ```