Add multiprocessing (#112)

* Add multiprocessing to the association study function
* Add multiprocessing to interaction tests
* Fix github actions
* Version 2.1.0

Author: jrm5100

.github/workflows/ci.yml

@@ -42,32 +42,46 @@ jobs:
           python-version: 3.7
 
       - name: Install Poetry
-        uses: snok/[email protected]
-
-      - name: Cache Poetry virtualenv
-        uses: actions/cache@v1
-        id: cache
+        uses: snok/[email protected]
         with:
-          path: ~/.virtualenvs
-          key: poetry-${{ hashFiles('**/poetry.lock') }}
-          restore-keys: |
-            poetry-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Set Poetry config
-        run: |
-          poetry config virtualenvs.in-project false
-          poetry config virtualenvs.path ~/.virtualenvs
-
-      - name: Install Dependencies
-        run: |
-          poetry install
-        if: steps.cache.outputs.cache-hit != 'true'
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      #----------------------------------------------
+      # install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction
+
+      #----------------------------------------------
+      # Activate Env
+      #----------------------------------------------
 
       - name: Code Quality
-        run: poetry run black . --check
+        run: |
+          source .venv/bin/activate
+          black . --check
 
       - name: Test with pytest
-        run: poetry run pytest -n 2 --cov . --cov-report=xml
+        run:  |
+          source .venv/bin/activate
+          pytest -n 2 --cov . --cov-report=xml
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

clarite/cli/commands/analyze.py

@@ -143,7 +143,6 @@ def ewas(
         covariates=covariates,
         data=data,
         survey_design_spec=sd,
-        cov_method=covariance_calc,
         min_n=min_n,
     )
     # Save
@@ -281,7 +280,6 @@ def ewas_r(
         covariates=covariates,
         data=data,
         survey_design_spec=sd,
-        cov_method=covariance_calc,
         min_n=min_n,
     )
     # Save

clarite/modules/analyze/regression/base.py

@@ -169,10 +169,13 @@ def _log_errors_and_warnings(self):
                 for warning in warning_list:
                     click.echo(click.style(f"\t{warning}", fg="yellow"))
 
-    def _check_covariate_values(self, keep_row_mask) -> Tuple[List[str], List[str]]:
+    @staticmethod
+    def _check_covariate_values(
+        data, covariates, keep_row_mask
+    ) -> Tuple[List[str], List[str]]:
         """Remove covariates that do not vary, warning when this occurs"""
         warnings = []
-        unique_values = self.data.loc[keep_row_mask, self.covariates].nunique()
+        unique_values = data.loc[keep_row_mask, covariates].nunique()
         varying_covars = list(unique_values[unique_values > 1].index.values)
         non_varying_covars = list(unique_values[unique_values <= 1].index.values)
         if len(non_varying_covars) > 0:
@@ -181,9 +184,6 @@ def _check_covariate_values(self, keep_row_mask) -> Tuple[List[str], List[str]]:
             )
         return varying_covars, warnings
 
-    def _encode_var_name(self, varname):
-        """Replace variable names"""
-
     @abstractmethod
     def run(self) -> None:
         """Run the regression"""