fix(build): fix optional poetry dependencies

Optional pip dependencies were configured incorrectly and were always being installed. The dependencies have been reconfigured as optional and included in the expected "extras" groups.

Fixes #335

.devcontainer/postCreateCommand.sh

@@ -1,4 +1,4 @@
 #! /usr/bin/env bash
 poetry config virtualenvs.in-project true --local
-poetry install --with cell_locations,collate,dev
+poetry install --with dev --all-extras
 poetry run pre-commit install --install-hooks

.github/workflows/codecov.yml

@@ -35,16 +35,10 @@ jobs:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
       #----------------------------------------------
-      # install dependencies if cache does not exist
+      # install dependencies
       #----------------------------------------------
       - 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
+        run: poetry install --no-interaction --all-extras --with dev
       #----------------------------------------------
       #    run test suite and output coverage file
       #----------------------------------------------

.github/workflows/pytest.yml

@@ -47,16 +47,10 @@ jobs:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ 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 --all-extras --without docs
-      #----------------------------------------------
       # install pycytominer
       #----------------------------------------------
-      - name: Install library
-        run: poetry install --no-interaction --only-root
+      - name: Install dependencies
+        run: poetry install --no-interaction --all-extras --with dev
       #----------------------------------------------
       #    run test suite and output coverage file
       #----------------------------------------------