Feat/use black lint (#716)

* blacklinter * format with black * add black to dev list * black * more formatting * python version to 3.7.9 * fix python version * remove python matrix * remove container workflows temporarily * remove fixed version for pip * changelog * fix black version * lock black linter version in action * black lint it * install dev requirments after installing balsamic * pytest dev install as its own step * unique name for pytest step * bring back container workflows * review comments * update docs
Clinical-Genomics · Aug 25, 2021 · a629fc3 · a629fc3
1 parent 5b0a4b4
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diff --git a/.github/workflows/black_linter.yml b/.github/workflows/black_linter.yml
@@ -0,0 +1,14 @@
+name: Black linter and code formatter
+on: [pull_request]
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+      - uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          version: "21.7b0"
diff --git a/.github/workflows/pytest_and_coveralls.yml b/.github/workflows/pytest_and_coveralls.yml
@@ -14,8 +14,6 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       fail-fast: false
-      matrix:
-        python-version: [3.6]
     steps:
       # Checkout BALSAMIC
       - name: Git checkout
@@ -33,15 +31,20 @@ jobs:
         with:
           activate-environment: balsamic
           environment-file: BALSAMIC/conda/balsamic.yaml
-          python-version: ${{ matrix.python-version }}
       # Install BALSAMIC
       - name: Install BALSAMIC
         id: install_balsamic
         shell: bash -l {0}
+        run: |
+          conda activate balsamic
+          pip install --no-cache-dir .
+      # Install pytest coveralls dependencies 
+      - name: Install PyTest and Coveralls
+        id: install_pytest
+        shell: bash -l {0}
         run: |
           conda activate balsamic
           pip install --no-cache-dir -r requirements-dev.txt
-          pip install .
       # Run PyTest
       - name: Run PyTest
         id: pytest

diff --git a/.style.yapf b/.style.yapf
diff --git a/BALSAMIC/__init__.py b/BALSAMIC/__init__.py
@@ -1 +1 @@
-__version__ = '7.2.6'
+__version__ = "7.2.6"
diff --git a/BALSAMIC/__version__.py b/BALSAMIC/__version__.py
@@ -1 +1 @@
-__version__ = '7.2.6'
+__version__ = "7.2.6"
diff --git a/BALSAMIC/assets/__init__.py b/BALSAMIC/assets/__init__.py
@@ -2,8 +2,8 @@
 
 ##### FILES #####
 
-cg_logo = 'assets/cg.png'
+cg_logo = "assets/cg.png"
 
 ##### Paths #####
 
-cg_logo_path = pkg_resources.resource_filename('BALSAMIC', cg_logo)
+cg_logo_path = pkg_resources.resource_filename("BALSAMIC", cg_logo)
diff --git a/BALSAMIC/commands/base.py b/BALSAMIC/commands/base.py
@@ -19,48 +19,42 @@
 from BALSAMIC import __version__
 
 LOG = logging.getLogger(__name__)
-LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
 
 @click.group()
-@click.option('--loglevel',
-              default='DEBUG',
-              type=click.Choice(LOG_LEVELS),
-              help="Set the level of log output.",
-              show_default=True)
+@click.option(
+    "--loglevel",
+    default="DEBUG",
+    type=click.Choice(LOG_LEVELS),
+    help="Set the level of log output.",
+    show_default=True,
+)
 @click.version_option(version=__version__)
 @click.pass_context
-@doc("""BALSAMIC {version}: Bioinformatic Analysis pipeLine for
-        SomAtic MutatIons in Cancer""".format(version=__version__))
+@doc(
+    """BALSAMIC {version}: Bioinformatic Analysis pipeLine for
+        SomAtic MutatIons in Cancer""".format(
+        version=__version__
+    )
+)
 def cli(context, loglevel):
     "BALSAMIC"
     coloredlogs.DEFAULT_FIELD_STYLES = {
-        'asctime': {
-            'color': 'green'
-        },
-        'hostname': {
-            'color': 'magenta'
-        },
-        'levelname': {
-            'color': 'yellow',
-            'bold': True
-        },
-        'programname': {
-            'color': 'cyan'
-        },
-        'name': {
-            'color': 'blue'
-        }
+        "asctime": {"color": "green"},
+        "hostname": {"color": "magenta"},
+        "levelname": {"color": "yellow", "bold": True},
+        "programname": {"color": "cyan"},
+        "name": {"color": "blue"},
     }
     coloredlogs.install(
         level=loglevel,
-        fmt=
-        '%(programname)s %(hostname)s %(asctime)s %(name)s pid:%(process)d [%(levelname)s] %(message)s'
+        fmt="%(programname)s %(hostname)s %(asctime)s %(name)s pid:%(process)d [%(levelname)s] %(message)s",
     )
     LOG.info("Running BALSAMIC version %s", __version__)
 
     context.obj = {}
-    context.obj['loglevel'] = loglevel
+    context.obj["loglevel"] = loglevel
     # LOG.info(f"BALSAMIC started with log level {loglevel}.")
 
 

diff --git a/BALSAMIC/commands/config/base.py b/BALSAMIC/commands/config/base.py
@@ -4,6 +4,7 @@
 from BALSAMIC.commands.config.case import case_config as case_command
 from BALSAMIC.commands.config.pon import pon_config as pon_command
 
+
 @click.group()
 @click.pass_context
 def config(context):