Update docs and tests to indicate Python3.5 support. (#106)

* Update docs and tests to indicate Python3.5 support.

* Disable Lint tests for Python3.5 since black doesn't support it.

* Syntax in YAML.

* Comprimise test requirements for Py3.5

* json.loads does NOT support bytes in Python3.5.

* Explicitly define the codecov tagets.

Author: rexwangcc

.github/workflows/pr-tests.yml

@@ -13,40 +13,46 @@ jobs:
     strategy:
       max-parallel: 16
       matrix:
-        python-version: [ '3.6', '3.7' ]
-        os: [ ubuntu-latest, macos-latest ]
+        python-version: ["3.6", "3.7", "3.5"]
+        os: [ubuntu-latest, macos-latest]
     steps:
-    - name: Checkout
-      uses: actions/checkout@v2
-      with:
-        ref: ${{ github.event.pull_request.head.sha }}
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
-    - name: Setup Python env
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-        architecture: x64
+      - name: Setup Python env
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements-test.txt -r requirements.txt
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-test.txt -r requirements.txt
 
-    - name: Lint Tests
-      run: |
-        # Check Black code style compliance
-        black ./ --skip-string-normalization --check
-        # Check PEP-8 compliance
-        flake8
+      - name: Lint Tests
+        # Black does not support Python3.5
+        # It will run on 3.6+, so we can
+        # safely disable it for 3.5 env
+        if: matrix.python-version != '3.5'
+        run: |
+          # Install black only for Py3.6+
+          pip install black==19.10b0
+          # Check Black code style compliance
+          black ./ --skip-string-normalization --check
+          # Check PEP-8 compliance
+          flake8
 
-    - name: Unit Tests
-      run: |
-        pytest --cov=cromwell_tools --cov-report=xml cromwell_tools/tests
+      - name: Unit Tests
+        run: |
+          pytest --cov=cromwell_tools --cov-report=xml cromwell_tools/tests
 
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        flags: unittests
-        name: Cromwell-tools Test Coverage
-        fail_ci_if_error: false  # See https://github.com/codecov/codecov-action/issues/29
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests
+          name: Cromwell-tools Test Coverage
+          fail_ci_if_error: false # See https://github.com/codecov/codecov-action/issues/29

.pre-commit-config.yaml

@@ -3,6 +3,7 @@ repos:
     rev: 19.10b0
     hooks:
     - id: black
+      # Note: this does NOT support Python3.5!
       language_version: python3
       # Using args here is not recommended by Black:
       # https://black.readthedocs.io/en/stable/version_control_integration.html

README.rst

@@ -21,8 +21,8 @@ Cromwell-tools
     :target: https://img.shields.io/github/license/broadinstitute/cromwell-tools.svg?style=flat-square
     :alt: License
 
-.. image:: https://img.shields.io/badge/python-3.6|3.7-green.svg?style=flat-square&logo=python&colorB=blue
-    :target: https://img.shields.io/badge/python-3.6|3.7-green.svg?style=flat-square&logo=python&colorB=blue
+.. image:: https://img.shields.io/badge/python-3.5|3.6|3.7-green.svg?style=flat-square&logo=python&colorB=blue
+    :target: https://img.shields.io/badge/python-3.5|3.6|3.7-green.svg?style=flat-square&logo=python&colorB=blue
     :alt: Language
 
 .. image:: https://img.shields.io/badge/Code%20Style-black-000000.svg?style=flat-square

codecov.yml

@@ -0,0 +1,29 @@
+codecov:
+  require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project: # settings affecting project coverage
+      default:
+        target: auto # auto % coverage target
+        threshold: 5% # allow for 5% reduction of coverage without failing
+
+    # do not run coverage on patch nor changes
+    patch: false
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "reach,diff,flags,tree"
+  behavior: default
+  require_changes: no

cromwell_tools/tests/test_utilities.py

@@ -450,11 +450,15 @@ def test_compose_oauth_options_for_jes_backend_cromwell_add_required_fields_to_w
         result_options = utils.compose_oauth_options_for_jes_backend_cromwell(
             test_auth, self.options_file_BytesIO
         )
-        result_options_in_dict = json.loads(result_options.getvalue())
+        # use .decode('utf-8') for Python3.5 compatibility
+        result_options_in_dict = json.loads(result_options.getvalue().decode('utf-8'))
 
         assert (
+            # use .decode('utf-8') for Python3.5 compatibility
             result_options_in_dict['read_from_cache']
-            == json.loads(self.options_file_BytesIO.getvalue())['read_from_cache']
+            == json.loads(self.options_file_BytesIO.getvalue().decode('utf-8'))[
+                'read_from_cache'
+            ]
         )
         assert (
             result_options_in_dict['google_project']
@@ -484,7 +488,8 @@ def test_if_compose_oauth_options_for_jes_backend_cromwell_can_deal_with_null_wo
         )
 
         result_options = utils.compose_oauth_options_for_jes_backend_cromwell(test_auth)
-        result_options_in_dict = json.loads(result_options.getvalue())
+        # use .decode('utf-8') for Python3.5 compatibility
+        result_options_in_dict = json.loads(result_options.getvalue().decode('utf-8'))
 
         assert (
             result_options_in_dict['google_project']

cromwell_tools/utilities.py

@@ -245,7 +245,8 @@ def validate_cromwell_label(
     elif isinstance(label_object, bytes):
         label_object = json.loads(label_object.decode('utf-8'))
     elif isinstance(label_object, io.BytesIO):
-        label_object = json.loads(label_object.getvalue())
+        # use .decode('utf-8') for Python3.5 compatibility
+        label_object = json.loads(label_object.getvalue().decode('utf-8'))
 
     for label_key, label_value in label_object.items():
         err_msg += _content_checker(_CROMWELL_LABEL_KEY_REGEX, label_key)
@@ -399,7 +400,8 @@ def compose_oauth_options_for_jes_backend_cromwell(
         cromwell_options_file = io.BytesIO(json.dumps({}).encode())
 
     # using `getvalue()` here so we don't have to seek back to the beginning if we need the value again
-    options_json = json.loads(cromwell_options_file.getvalue())
+    # use .decode('utf-8') for Python3.5 compatibility
+    options_json = json.loads(cromwell_options_file.getvalue().decode('utf-8'))
     google_project = auth.service_key_content['project_id']
 
     options_json.update(

requirements-test.txt

@@ -1,4 +1,3 @@
-black==19.10b0
 flake8==3.7.7
 mock>=2.0.0
 pre-commit==1.14.4