Add CI caching for python environments (#23)

* Added first pytest script for protein class and a script for performing local tests.

* Added pytest in CI

* Forgot -r for file

* Version of pytest with pytest at end of pipeline

* New pytest CI where pip installs local package

* Fixed tabs and added caching of python/pip environment

* Removed dot and added removal of build dirs to manage clean command

* Added cache ignores for env setup and ids for the caches

* Fixed cache IDs

* Renamed cache because GitHub does not allow for clearing caches...

* Moved python setup to be before cache loading

* Run that will install the dependencies

* Uncommented the cache-hit detection for installing dependencies

* Updated pre-commit version in hope that runner will create new cache

* Added more tests and added flake8 incompatability

* Other flake8 config try

* Reset to .flake8 file

* Downgrade of pre-commit to force dep. installation in CI

* Different pre-commit version

* Added depth_first tests

* Added depth_first_bnb tests

* Push to try and install all dependencies correctly

* Added back cache check for installing dependencies. New way of calling flake8, added class dependencies on tests

* Removed ls

* Core change test

* Core change test - new correctly

* Core archiving works

* Fixed pytest ordering and upgraded pandas version to trigger new cache

* Upgraded pandas

* Changed pandas version to 1.1.0

* Dependency check

* new flake8 installation

* Flake8 action

* Added pip update flag

* Cleaned up the flake8 action usage

* Trying to install new deps

* Removed caching, only using dependencies during pytest

.github/workflows/build_deploy.yml

@@ -22,29 +22,21 @@ jobs:
   syntax_check:
     name: Check for syntax errors
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.6]
-        os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
       - uses: actions/checkout@v2
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Flake8 - Error on syntax errors or undefined names
+        uses: py-actions/flake8@v1.1.0
         with:
-          python-version: ${{ matrix.python-version }}
+          args: --count --select=E9,F63,F7,F82 --show-source --statistics
+          update-pip: "true"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install flake8
-
-      - name: Lint with flake8
-        run: |
-          # Stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # Exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Flake8 - Warn on everything else
+        uses: py-actions/flake8@v1.1.0
+        with:
+          args: --count --exit-zero --max-complexity=10 --statistics
+          max-line-length: 127
+          update-pip: "true"
 
   pytest:
     name: Pytest
@@ -71,7 +63,6 @@ jobs:
       - name: Test with pytest
         run: pytest
 
-
   build_wheels:
     name: Build wheels
     needs: [pytest, matrix_prep]