lint: formatting

.github/workflows/deploy.yml

@@ -1,6 +1,7 @@
 name: deploy
 
 on:
+  pull_request: []
   push:
     branches:
       - master
@@ -9,17 +10,22 @@ jobs:
   docker-deploy:
     runs-on: ubuntu-latest
     env:
-      CONTAINER: quay.io/vanessa/cdb
+      CONTAINER: ghcr.io/vsoch/cdb
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Build Docker Image
         run: docker build -f Dockerfile.base -t "${CONTAINER}" .
-      - name: Log In to Quay.io
-        env:
-          DOCKER_USER: ${{ secrets.DOCKER_USER }}
-          DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
-        run: echo "${{ secrets.DOCKER_PASSWORD }}" | docker login quay.io -u ${{ secrets.DOCKER_USER }} --password-stdin
+
+      - name: GHCR Login
+        if: (github.event_name != 'pull_request')
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Tag and Push images
+        if: (github.event_name != 'pull_request')
         run: |
           DOCKER_TAG=$(docker run "${CONTAINER}:latest" --version)
           echo "Docker tag is: ${DOCKER_TAG}"

.github/workflows/main.yml

@@ -11,7 +11,7 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Setup black environment
         run: conda create --quiet --name black black pyflakes

Dockerfile

@@ -1,4 +1,4 @@
-FROM bitnami/minideb:stretch as generator
+FROM bitnami/minideb as generator
 # docker build -t data-container .
 ENV PATH /opt/conda/bin:${PATH}
 ENV LANG C.UTF-8

Dockerfile.base

@@ -1,4 +1,4 @@
-FROM bitnami/minideb:stretch as generator
+FROM bitnami/minideb as generator
 # docker build -t data-container .
 ENV PATH /opt/conda/bin:${PATH}
 ENV LANG C.UTF-8

cdb/client/__init__.py

@@ -40,19 +40,26 @@ def get_parser():
 
     description = "actions for cdb"
     subparsers = parser.add_subparsers(
-        help="cdb actions", title="actions", description=description, dest="command",
+        help="cdb actions",
+        title="actions",
+        description=description,
+        dest="command",
     )
 
     # print version and exit
     subparsers.add_parser("version", help="show software version")
 
     # Generate a key for the interface
     generate = subparsers.add_parser(
-        "generate", help="generate a template go script for container entrypoint.",
+        "generate",
+        help="generate a template go script for container entrypoint.",
     )
 
     generate.add_argument(
-        "path", help="Path to dataset files.", nargs="?", default=".",
+        "path",
+        help="Path to dataset files.",
+        nargs="?",
+        default=".",
     )
 
     # Specify output file, defaults to db.go
@@ -91,14 +98,13 @@ def get_parser():
 
 
 def main():
-    """main entrypoint for cdb
-    """
+    """main entrypoint for cdb"""
 
     parser = get_parser()
 
     def help(return_code=0):
-        """print help, including the software version and active client 
-           and exit with return code.
+        """print help, including the software version and active client
+        and exit with return code.
         """
         version = cdb.__version__
 

cdb/client/generate.py

@@ -12,7 +12,6 @@
 
 
 def main(args, extra):
-
     # Create a Container database
     db = ContainerDatabase(path=args.path)
     db.generate(

cdb/functions.py

@@ -13,7 +13,6 @@
 
 
 def basic(filename):
-    """Given a filename, return a dictionary with basic metadata about it
-    """
+    """Given a filename, return a dictionary with basic metadata about it"""
     st = os.stat(filename)
     return {"size": st.st_size, "sha256": get_file_hash(filename)}

cdb/logger/message.py

@@ -78,8 +78,8 @@ def success(self, message):
 
     def useColor(self):
         """useColor will determine if color should be added
-           to a print. Will check if being run in a terminal, and
-           if has support for asci
+        to a print. Will check if being run in a terminal, and
+        if has support for asci
         """
         COLORIZE = get_user_color_preference()
         if COLORIZE is not None:
@@ -94,7 +94,7 @@ def useColor(self):
 
     def addColor(self, level, text):
         """addColor to the prompt (usually prefix) if terminal
-           supports, and specified to do so
+        supports, and specified to do so
         """
         if self.colorize:
             if level in self.colors:
@@ -103,7 +103,7 @@ def addColor(self, level, text):
 
     def emitError(self, level):
         """determine if a level should print to
-           stderr, includes all levels but INFO and QUIET
+        stderr, includes all levels but INFO and QUIET
         """
         if level in [
             ABORT,
@@ -126,20 +126,19 @@ def emitOutput(self, level):
         return False
 
     def isEnabledFor(self, messageLevel):
-        """check if a messageLevel is enabled to emit a level
-        """
+        """check if a messageLevel is enabled to emit a level"""
         if messageLevel <= self.level:
             return True
         return False
 
     def emit(self, level, message, prefix=None, color=None):
         """emit is the main function to print the message
-           optionally with a prefix
+        optionally with a prefix
 
-           Arguments:
-            - level (int) : the level of the message
-            - message (str) : the message to print
-            - prefix (str) : a prefix for the message
+        Arguments:
+         - level (int) : the level of the message
+         - message (str) : the message to print
+         - prefix (str) : a prefix for the message
         """
         if color is None:
             color = level
@@ -172,15 +171,15 @@ def emit(self, level, message, prefix=None, color=None):
 
     def write(self, stream, message):
         """write will write a message to a stream,
-           first checking the encoding
+        first checking the encoding
         """
         if isinstance(message, bytes):
             message = message.decode("utf-8")
         stream.write(message)
 
     def get_logs(self, join_newline=True):
         """'get_logs will return the complete history, joined by newline
-            (default) or as is.
+        (default) or as is.
         """
         if join_newline:
             return "\n".join(self.history)
@@ -198,15 +197,14 @@ def show_progress(
         symbol=None,
     ):
         """create a terminal progress bar, default bar shows for verbose+
- 
-           Parameters
-           ==========
-           iteration: current iteration (Int)
-           total: total iterations (Int)
-           length: character length of bar (Int)
+
+        Parameters
+        ==========
+        iteration: current iteration (Int)
+        total: total iterations (Int)
+        length: character length of bar (Int)
         """
         if not self.level == QUIET:
-
             percent = 100 * (iteration / float(total))
             progress = int(length * iteration // total)
 
@@ -289,18 +287,17 @@ def debug(self, message):
         self.emit(DEBUG, message, "DEBUG")
 
     def is_quiet(self):
-        """is_quiet returns true if the level is under 1
-        """
+        """is_quiet returns true if the level is under 1"""
         if self.level < 1:
             return False
         return True
 
     # Terminal ------------------------------------------
 
     def table(self, rows, col_width=2):
-        """table will print a table of entries. If the rows is 
-           a dictionary, the keys are interpreted as column names. if
-           not, a numbered list is used.
+        """table will print a table of entries. If the rows is
+        a dictionary, the keys are interpreted as column names. if
+        not, a numbered list is used.
         """
 
         labels = [str(x) for x in range(1, len(rows) + 1)]
@@ -317,9 +314,9 @@ def table(self, rows, col_width=2):
 
 def get_logging_level():
     """get_logging_level will configure a logging to standard out based on
-        selected level, which should be in an environment variable called
-        MESSAGELEVEL. if MESSAGELEVEL is not set, the maximum level
-        (5) is assumed (all messages).
+    selected level, which should be in an environment variable called
+    MESSAGELEVEL. if MESSAGELEVEL is not set, the maximum level
+    (5) is assumed (all messages).
     """
     level = os.environ.get("CDB_MESSAGELEVEL", INFO)
 
@@ -361,7 +358,7 @@ def get_user_color_preference():
 
 def convert2boolean(arg):
     """convert2boolean is used for environmental variables that must be
-       returned as boolean
+    returned as boolean
     """
     if not isinstance(arg, bool):
         return arg.lower() in ("yes", "true", "t", "1", "y")

cdb/main/__init__.py

@@ -26,30 +26,28 @@
 
 class ContainerDatabase:
     """A container database metadata generator will take some input folder
-       of files, and recursively run a user-provided or cdb-provided function
-       to extract metadata for each one. If no custom function is provided,
-       we provide basic metadata about file versions.
+    of files, and recursively run a user-provided or cdb-provided function
+    to extract metadata for each one. If no custom function is provided,
+    we provide basic metadata about file versions.
     """
 
     def __init__(self, path, pattern="*"):
-        """extract metadata for some recursive set of data objects
-        """
+        """extract metadata for some recursive set of data objects"""
         self.get_files(path, pattern)
         self.path = path
         self.pattern = pattern
         self.metadata = {}
 
     def get_files(self, path, pattern="*"):
-        """return files, given update path and pattern
-        """
+        """return files, given update path and pattern"""
         self.path = path
         self.pattern = pattern
         return self.files
 
     @property
     def files(self):
         """Given a path, check that it exists, and then create an iterator
-           to go over files.
+        to go over files.
         """
         if self.path in [".", None]:
             self.path = os.getcwd()
@@ -59,8 +57,8 @@ def files(self):
 
     def generate(self, output=None, template="db.go", force=False, func=None):
         """Given an output file name and a template, iterate
-           through files and generate the in-memory database golang file to
-           compile into a container.
+        through files and generate the in-memory database golang file to
+        compile into a container.
         """
         bot.debug(f"Loading template {template}")
         template = get_template(template)
@@ -91,13 +89,11 @@ def generate(self, output=None, template="db.go", force=False, func=None):
         return script
 
     def export_dockerfile(self, name="Dockerfile"):
-        """export a Dockerfile that will perform a multistage build to
-        """
+        """export a Dockerfile that will perform a multistage build to"""
         pass
 
     def get_function(self, funcname=None):
-        """Given a function name, return it. Exit on error if not found.
-        """
+        """Given a function name, return it. Exit on error if not found."""
         # Default to cdb.functions.basic
         funcname = funcname or "basic"
 

cdb/templates/__init__.py

@@ -16,8 +16,8 @@
 
 def get_template(name, load=True):
     """Given the name of a template (a go file to use to generate the dataset
-       metadata) return the template path if it exists. Otherwise, exit on
-       error
+    metadata) return the template path if it exists. Otherwise, exit on
+    error
     """
     # The user can provide a custom template, must have {{ updates }} to include
     if not os.path.exists(name):