Remove empty default values for inputs/outputs arguments

docs/faq.rst

@@ -45,7 +45,7 @@ How can I make an App dependent on multiple inputs?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You can pass any number of futures in to a single App either as positional arguments
-or as a list of futures via the special keyword ``inputs=()``.
+or as a list of futures via the special keyword ``inputs``.
 The App will wait for all inputs to be satisfied before execution.
 
 

docs/historical/changelog.rst

@@ -301,7 +301,7 @@ New Functionality
    .. code-block:: python
 
       @bash_app
-      def cat(inputs=(), outputs=()):
+      def cat(inputs, outputs):
            return 'cat {} > {}'.format(inputs[0], outputs[0])
 
       concat = cat(inputs=['hello-0.txt'],
@@ -314,7 +314,7 @@ New Functionality
       from parsl import File
 
       @bash_app
-      def cat(inputs=(), outputs=()):
+      def cat(inputs, outputs):
            return 'cat {} > {}'.format(inputs[0].filepath, outputs[0].filepath)
 
       concat = cat(inputs=[File('hello-0.txt')],
@@ -328,7 +328,7 @@ New Functionality
       from parsl import File
 
       @bash_app
-      def cat(inputs=(), outputs=()):
+      def cat(inputs, outputs):
            return 'cat {} > {}'.format(inputs[0].filepath, outputs[0].filepath)
 
 
@@ -409,16 +409,16 @@ New Functionality
 
         # The following example worked until v0.8.0
         @bash_app
-        def cat(inputs=(), outputs=()):
+        def cat(inputs, outputs):
             return 'cat {inputs[0]} > {outputs[0]}' # <-- Relies on Parsl auto formatting the string
 
         # Following are two mechanisms that will work going forward from v0.9.0
         @bash_app
-        def cat(inputs=(), outputs=()):
+        def cat(inputs, outputs):
             return 'cat {} > {}'.format(inputs[0], outputs[0]) # <-- Use str.format method
 
         @bash_app
-        def cat(inputs=(), outputs=()):
+        def cat(inputs, outputs):
             return f'cat {inputs[0]} > {outputs[0]}' # <-- OR use f-strings introduced in Python3.6
 
 
@@ -522,12 +522,12 @@ New Functionality
 
      # Old style: " ".join(inputs) is legal since inputs will behave like a list of strings
      @bash_app
-     def concat(inputs=(), outputs=(), stdout="stdout.txt", stderr='stderr.txt'):
+     def concat(inputs, outputs, stdout="stdout.txt", stderr='stderr.txt'):
          return "cat {0} > {1}".format(" ".join(inputs), outputs[0])
 
      # New style:
      @bash_app
-     def concat(inputs=(), outputs=(), stdout="stdout.txt", stderr='stderr.txt'):
+     def concat(inputs, outputs, stdout="stdout.txt", stderr='stderr.txt'):
          return "cat {0} > {1}".format(" ".join(list(map(str,inputs))), outputs[0])
 
 * Cleaner user app file log management.

docs/userguide/apps/python.rst

@@ -196,7 +196,7 @@ Some keyword arguments to the Python function are treated differently by Parsl
         return x * 2
 
     @python_app()
-    def reduce_app(inputs = ()):
+    def reduce_app(inputs):
         return sum(inputs)
 
     map_futures = [map_app(x) for x in range(3)]
@@ -212,7 +212,7 @@ Some keyword arguments to the Python function are treated differently by Parsl
 .. code-block:: python
 
     @python_app()
-    def write_app(message, outputs=()):
+    def write_app(message, outputs):
         """Write a single message to every file in outputs"""
         for path in outputs:
             with open(path, 'w') as fp:

docs/userguide/configuration/data.rst

@@ -67,7 +67,7 @@ irrespective of where that app executes.
 .. code-block:: python
 
     @python_app
-    def print_file(inputs=()):
+    def print_file(inputs):
         with open(inputs[0].filepath, 'r') as inp:
             content = inp.read()
             return(content)
@@ -189,7 +189,7 @@ The following example illustrates how the remote file is implicitly downloaded f
 .. code-block:: python
 
     @python_app
-    def convert(inputs=(), outputs=()):
+    def convert(inputs, outputs):
         with open(inputs[0].filepath, 'r') as inp:
             content = inp.read()
             with open(outputs[0].filepath, 'w') as out:

docs/userguide/configuration/execution.rst

@@ -216,12 +216,12 @@ The following code snippet shows how apps can specify suitable executors in the
 
      # A mock molecular dynamics simulation app
      @bash_app(executors=["Theta.Phi"])
-     def MD_Sim(arg, outputs=()):
+     def MD_Sim(arg, outputs):
          return "MD_simulate {} -o {}".format(arg, outputs[0])
 
      # Visualize results from the mock MD simulation app
      @bash_app(executors=["Cooley.GPU"])
-     def visualize(inputs=(), outputs=()):
+     def visualize(inputs, outputs):
          bash_array = " ".join(inputs)
          return "viz {} -o {}".format(bash_array, outputs[0])
 

docs/userguide/workflows/futures.rst

@@ -151,7 +151,7 @@ be created (``hello.outputs[0].result()``).
       # This app echoes the input string to the first file specified in the
       # outputs list
       @bash_app
-      def echo(message, outputs=()):
+      def echo(message, outputs):
           return 'echo {} &> {}'.format(message, outputs[0])
 
       # Call echo specifying the output file

docs/userguide/workflows/workflow.rst

@@ -63,7 +63,7 @@ Sequential workflows can be created by passing an AppFuture from one task to ano
 
       # Write a message to a file
       @bash_app
-      def save(message, outputs=()):
+      def save(message, outputs):
             return 'echo {} &> {}'.format(message, outputs[0])
 
       message = generate(10)
@@ -159,15 +159,15 @@ In other cases, it can be convenient to pass data in files, as in the following
       parsl.load()
 
       @bash_app
-      def generate(outputs=()):
+      def generate(outputs):
           return 'echo $(( RANDOM % (10 - 5 + 1 ) + 5 )) &> {}'.format(outputs[0])
 
       @bash_app
-      def concat(inputs=(), outputs=(), stdout='stdout.txt', stderr='stderr.txt'):
+      def concat(inputs, outputs, stdout='stdout.txt', stderr='stderr.txt'):
           return 'cat {0} >> {1}'.format(' '.join(inputs), outputs[0])
 
       @python_app
-      def total(inputs=()):
+      def total(inputs):
           total = 0
           with open(inputs[0].filepath, 'r') as f:
               for l in f:
@@ -209,7 +209,7 @@ the sum of those results.
 
     # Reduce function that returns the sum of a list
     @python_app
-    def app_sum(inputs=()):
+    def app_sum(inputs):
         return sum(inputs)
 
     # Create a list of integers

parsl/app/bash.py

@@ -96,7 +96,7 @@ def open_std_fd(fdname):
     # TODO : Add support for globs here
 
     missing = []
-    for outputfile in kwargs.get('outputs', []):
+    for outputfile in kwargs.get('outputs') or []:
         fpath = outputfile.filepath
 
         if not os.path.exists(fpath):

parsl/data_provider/ftp.py

@@ -66,7 +66,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def _ftp_stage_in(working_dir, parent_fut=None, outputs=[], _parsl_staging_inhibit=True):
+def _ftp_stage_in(working_dir, *, parent_fut=None, outputs, _parsl_staging_inhibit=True):
     file = outputs[0]
     if working_dir:
         os.makedirs(working_dir, exist_ok=True)

parsl/data_provider/globus.py

@@ -267,7 +267,7 @@ def _update_local_path(self, file, executor, dfk):
 # this cannot be a class method, but must be a function, because I want
 # to be able to use partial() on it - and partial() does not work on
 # class methods
-def _globus_stage_in(provider, executor, parent_fut=None, outputs=[], _parsl_staging_inhibit=True):
+def _globus_stage_in(provider, executor, *, parent_fut=None, outputs, _parsl_staging_inhibit=True):
     globus_ep = provider._get_globus_endpoint(executor)
     file = outputs[0]
     dst_path = os.path.join(
@@ -280,7 +280,7 @@ def _globus_stage_in(provider, executor, parent_fut=None, outputs=[], _parsl_sta
             file.path, dst_path)
 
 
-def _globus_stage_out(provider, executor, app_fu, inputs=[], _parsl_staging_inhibit=True):
+def _globus_stage_out(provider, executor, *, app_fu, inputs, _parsl_staging_inhibit=True):
     """
     Although app_fu isn't directly used in the stage out code,
     it is needed as an input dependency to ensure this code

parsl/data_provider/http.py

@@ -73,7 +73,7 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def _http_stage_in(working_dir, parent_fut=None, outputs=[], _parsl_staging_inhibit=True):
+def _http_stage_in(working_dir, *, parent_fut=None, outputs, _parsl_staging_inhibit=True):
     file = outputs[0]
     if working_dir:
         os.makedirs(working_dir, exist_ok=True)

parsl/data_provider/zip.py

@@ -96,7 +96,7 @@ def stage_in(self, dm, executor, file, parent_fut):
         return app_fut._outputs[0]
 
 
-def _zip_stage_out(zip_file, inside_path, working_dir, parent_fut=None, inputs=[], _parsl_staging_inhibit=True):
+def _zip_stage_out(zip_file, inside_path, working_dir, *, parent_fut=None, inputs, _parsl_staging_inhibit=True):
     file = inputs[0]
 
     os.makedirs(os.path.dirname(zip_file), exist_ok=True)

parsl/dataflow/dflow.py

@@ -782,7 +782,7 @@ def _add_input_deps(self, executor: str, args: Sequence[Any], kwargs: Dict[str,
             logger.debug("Not performing input staging")
             return args, kwargs, func
 
-        inputs = kwargs.get('inputs', [])
+        inputs = kwargs.get('inputs') or []
         for idx, f in enumerate(inputs):
             (inputs[idx], func) = self.data_manager.optionally_stage_in(f, func, executor)
 
@@ -801,7 +801,7 @@ def _add_input_deps(self, executor: str, args: Sequence[Any], kwargs: Dict[str,
 
     def _add_output_deps(self, executor: str, args: Sequence[Any], kwargs: Dict[str, Any], app_fut: AppFuture, func: Callable) -> Callable:
         logger.debug("Adding output dependencies")
-        outputs = kwargs.get('outputs', [])
+        outputs = kwargs.get('outputs') or []
         app_fut._outputs = []
 
         # Pass over all possible outputs: the outputs kwarg, stdout and stderr
@@ -884,7 +884,7 @@ def check_dep(d: Any) -> None:
             check_dep(dep)
 
         # Check for futures in inputs=[<fut>...]
-        for dep in kwargs.get('inputs', []):
+        for dep in kwargs.get('inputs') or []:
             check_dep(dep)
 
         return depends
@@ -932,7 +932,7 @@ def append_failure(e: Exception, dep: Future) -> None:
                 append_failure(e, dep)
 
         # Check for futures in inputs=[<fut>...]
-        if 'inputs' in kwargs:
+        if kwargs.get('inputs'):
             new_inputs = []
             for dep in kwargs['inputs']:
                 try:

parsl/dataflow/memoization.py

@@ -191,7 +191,7 @@ def make_hash(self, task: TaskRecord) -> str:
             logger.debug("Ignoring kwarg %s", k)
             del filtered_kw[k]
 
-        if 'outputs' in task['kwargs']:
+        if task['kwargs'].get('outputs'):
             outputs = task['kwargs']['outputs']
             del filtered_kw['outputs']
             t.append(id_for_memo(outputs, output_ref=True))

parsl/executors/radical/executor.py

@@ -422,9 +422,9 @@ def task_translate(self, tid, func, parsl_resource_specification, args, kwargs):
                 task.use_mpi = False
                 task.function = self._pack_and_apply_message(func, args, kwargs)
 
-        task.input_staging = self._stage_files(kwargs.get("inputs", []),
+        task.input_staging = self._stage_files(kwargs.get("inputs") or [],
                                                mode='in')
-        task.output_staging = self._stage_files(kwargs.get("outputs", []),
+        task.output_staging = self._stage_files(kwargs.get("outputs") or [],
                                                 mode='out')
 
         task.input_staging.extend(self._stage_files(list(args), mode='in'))

parsl/executors/taskvine/executor.py

@@ -360,8 +360,8 @@ def submit(self, func, resource_specification, *args, **kwargs):
 
         # Determine whether to stage input files that will exist at the workers
         # Input and output files are always cached
-        input_files += [self._register_file(f) for f in kwargs.get("inputs", []) if isinstance(f, File)]
-        output_files += [self._register_file(f) for f in kwargs.get("outputs", []) if isinstance(f, File)]
+        input_files += [self._register_file(f) for f in kwargs.get("inputs") or [] if isinstance(f, File)]
+        output_files += [self._register_file(f) for f in kwargs.get("outputs") or [] if isinstance(f, File)]
 
         # Also consider any *arg that looks like a file as an input:
         input_files += [self._register_file(f) for f in args if isinstance(f, File)]

parsl/executors/taskvine/install-taskvine.sh

@@ -12,7 +12,7 @@ TARBALL="cctools-$CCTOOLS_VERSION-x86_64-ubuntu20.04.tar.gz"
 
 # If stderr is *not* a TTY, then disable progress bar and show HTTP response headers
 [[ ! -t 1 ]] && NO_VERBOSE="--no-verbose" SHOW_HEADERS="-S"
-wget "$NO_VERBOSE" "$SHOW_HEADERS" -O /tmp/cctools.tar.gz "https://github.com/cooperative-computing-lab/cctools/releases/download/release/$CCTOOLS_VERSION/$TARBALL"
+wget $NO_VERBOSE $SHOW_HEADERS -O /tmp/cctools.tar.gz "https://github.com/cooperative-computing-lab/cctools/releases/download/release/$CCTOOLS_VERSION/$TARBALL"
 
 mkdir -p /tmp/cctools
 tar -C /tmp/cctools -zxf /tmp/cctools.tar.gz --strip-components=1

parsl/executors/workqueue/executor.py

@@ -461,8 +461,8 @@ def submit(self, func, resource_specification, *args, **kwargs):
         output_files = []
 
         # Determine the input and output files that will exist at the workers:
-        input_files += [self._register_file(f) for f in kwargs.get("inputs", []) if isinstance(f, File)]
-        output_files += [self._register_file(f) for f in kwargs.get("outputs", []) if isinstance(f, File)]
+        input_files += [self._register_file(f) for f in kwargs.get("inputs") or [] if isinstance(f, File)]
+        output_files += [self._register_file(f) for f in kwargs.get("outputs") or [] if isinstance(f, File)]
 
         # Also consider any *arg that looks like a file as an input:
         input_files += [self._register_file(f) for f in args if isinstance(f, File)]

parsl/tests/integration/test_parsl_load_default_config.py

@@ -3,7 +3,7 @@
 
 
 @python_app
-def cpu_stress(inputs=[], outputs=[]):
+def cpu_stress(inputs=None, outputs=None):
     s = 0
     for i in range(10**8):
         s += i

parsl/tests/test_aalst_patterns.py

@@ -76,7 +76,7 @@ def slow_increment(x, dur=1):
 
 
 @python_app
-def join(inputs=[]):
+def join(inputs):
     return sum(inputs)
 
 

parsl/tests/test_bash_apps/test_apptimeout.py

@@ -7,7 +7,7 @@
 
 
 @bash_app
-def echo_to_file(inputs=(), outputs=(), walltime=0.01):
+def echo_to_file(inputs=None, outputs=None, walltime=0.01):
     return """echo "sleeping"; sleep 0.05"""
 
 

parsl/tests/test_bash_apps/test_basic.py

@@ -11,7 +11,7 @@
 
 
 @bash_app
-def echo_to_file(inputs=(), outputs=(), stderr=None, stdout=None):
+def echo_to_file(inputs, outputs, stderr=None, stdout=None):
     res = ""
     for o in outputs:
         for i in inputs:

parsl/tests/test_bash_apps/test_memoize.py

@@ -5,7 +5,7 @@
 
 
 @bash_app(cache=True)
-def fail_on_presence(outputs=()):
+def fail_on_presence(outputs):
     return 'if [ -f {0} ] ; then exit 1 ; else touch {0}; fi'.format(outputs[0])
 
 
@@ -23,7 +23,7 @@ def test_bash_memoization(tmpd_cwd, n=2):
 
 
 @bash_app(cache=True)
-def fail_on_presence_kw(outputs=(), foo=None):
+def fail_on_presence_kw(outputs, foo=None):
     return 'if [ -f {0} ] ; then exit 1 ; else touch {0}; fi'.format(outputs[0])
 
 

parsl/tests/test_bash_apps/test_multiline.py

@@ -5,7 +5,7 @@
 
 
 @bash_app
-def multiline(inputs=(), outputs=(), stderr=None, stdout=None):
+def multiline(inputs, outputs, stderr=None, stdout=None):
     return """echo {inputs[0]} &> {outputs[0]}
     echo {inputs[1]} &> {outputs[1]}
     echo {inputs[2]} &> {outputs[2]}

parsl/tests/test_bash_apps/test_pipeline.py

@@ -6,7 +6,7 @@
 
 
 @bash_app
-def increment(inputs=(), outputs=(), stdout=None, stderr=None):
+def increment(inputs, outputs, stdout=None, stderr=None):
     cmd_line = """
     if ! [ -f {inputs[0]} ] ; then exit 43 ; fi
     x=$(cat {inputs[0]})
@@ -16,7 +16,7 @@ def increment(inputs=(), outputs=(), stdout=None, stderr=None):
 
 
 @bash_app
-def slow_increment(dur, inputs=(), outputs=(), stdout=None, stderr=None):
+def slow_increment(dur, inputs, outputs, stdout=None, stderr=None):
     cmd_line = """
     x=$(cat {inputs[0]})
     echo $(($x+1)) > {outputs[0]}