Type hinting and misc changes

docs/configuring_cylc.md

@@ -11,3 +11,5 @@ Additionally `cylc` uses a file called `$HOME/.cylc/flow/global.cylc` to control
 **WARNING:**
 The contents of the above two files will be platform specific.
 ---
+
+See [Configuring Cylc Discover](platforms/configuring_cylc_discover.md) for instructions on configuring cylc for Discover.

docs/examples/description.md

@@ -24,7 +24,7 @@ experiment_id: {suite_name}-suite
 ```
 
 `swell create` also contains argument inputs. For instance, `-p` or `--platform` allows
-user to pick which platform they would like to run on.
+user to pick which platform they would like to run on. If unspecified, swell will run on SLES15 by default.
 
 ```bash
 swell create 3dvar -p nccs_discover_sles15
@@ -113,4 +113,4 @@ dependencies. For each suite, this will have a different structure and different
 
 `experiment.yaml`: This is the key configuration file that dictates the inputs for contain configuration variables that will be used for different scripts in the workflow.
 
-For each JEDI bundle type (i.e., fv3-jedi, soca) and suite (3dvar, hofx etc.) in this section, we will display the `experiment.yaml` and talk about details.
+For each JEDI bundle type (i.e., fv3-jedi, soca) and suite (3dvar, hofx etc.) in this section, we will display the `experiment.yaml` and talk about details.

docs/installing_swell.md

@@ -29,4 +29,6 @@ cd swell
 pip install --prefix=/path/to/install/swell/ .
 ```
 
-To make the software useable ensure `/path/to/install/swell/bin` is in the `$PATH`. Also ensure that `/path/to/install/swell/lib/python<version>/site-packages` is in the `$PYTHONPATH`, where `<version>` denotes the version of Python used for the install, e.g. `3.9`.
+To make the software usable ensure `/path/to/install/swell/bin` is in the `$PATH`. Also ensure that `/path/to/install/swell/lib/python<version>/site-packages` is in the `$PYTHONPATH`, where `<version>` denotes the version of Python used for the install, e.g. `3.9`.
+
+Swell makes use of additional packages which are located in shared directories on Discover, such as under `/discover/nobackup/projects/gmao`. When installed correctly, many of these libraries should be visible in the `$PYTHONPATH`.

src/swell/deployment/create_experiment.py

@@ -15,6 +15,8 @@
 import sys
 import yaml
 
+from typing import Union, Optional
+
 from swell.deployment.prepare_config_and_suite.prepare_config_and_suite import \
      PrepareExperimentConfigAndSuite
 from swell.swell_path import get_swell_path
@@ -27,8 +29,13 @@
 # --------------------------------------------------------------------------------------------------
 
 
-def clone_config(configuration, experiment_id, method, platform, advanced):
-
+def clone_config(
+    configuration: str,
+    experiment_id: str,
+    method: str,
+    platform: str,
+    advanced: bool
+) -> str:
     # Create a logger
     logger = Logger('SwellCloneExperiment')
 
@@ -59,7 +66,14 @@ def clone_config(configuration, experiment_id, method, platform, advanced):
 # --------------------------------------------------------------------------------------------------
 
 
-def prepare_config(suite, method, platform, override, advanced, slurm):
+def prepare_config(
+    suite: str,
+    method: str,
+    platform: str,
+    override: Union[dict, str, None],
+    advanced: bool,
+    slurm: str
+) -> str:
 
     # Create a logger
     # ---------------
@@ -136,13 +150,21 @@ def prepare_config(suite, method, platform, override, advanced, slurm):
 
     # Return path to dictionary file
     # ------------------------------
+
     return experiment_dict_string_comments
 
 
 # --------------------------------------------------------------------------------------------------
 
 
-def create_experiment_directory(suite, method, platform, override, advanced, slurm):
+def create_experiment_directory(
+    suite: str,
+    method: str,
+    platform: str,
+    override: str,
+    advanced: bool,
+    slurm: str
+) -> None:
 
     # Create a logger
     # ---------------
@@ -187,10 +209,10 @@ def create_experiment_directory(suite, method, platform, override, advanced, slu
     # Copy suite and platform files to experiment suite directory
     # -----------------------------------------------------------
     swell_suite_path = os.path.join(get_swell_path(), 'suites', suite)
-    copy_platform_files(logger, exp_suite_path, platform)
+    copy_platform_files(exp_suite_path, platform)
 
     if os.path.exists(os.path.join(swell_suite_path, 'eva')):
-        copy_eva_files(logger, swell_suite_path, exp_suite_path)
+        copy_eva_files(swell_suite_path, exp_suite_path)
 
     # Set the swell paths in the modules file and create csh versions
     # ---------------------------------------------------------------
@@ -217,7 +239,10 @@ def create_experiment_directory(suite, method, platform, override, advanced, slu
 # --------------------------------------------------------------------------------------------------
 
 
-def copy_eva_files(logger, swell_suite_path, exp_suite_path):
+def copy_eva_files(
+    swell_suite_path: str,
+    exp_suite_path: str
+) -> None:
 
     # Repo eva files
     eva_directory = os.path.join(swell_suite_path, 'eva')
@@ -236,7 +261,11 @@ def copy_eva_files(logger, swell_suite_path, exp_suite_path):
 # --------------------------------------------------------------------------------------------------
 
 
-def copy_platform_files(logger, exp_suite_path, platform=None):
+def copy_platform_files(
+    logger: Logger,
+    exp_suite_path: str,
+    platform: Optional[str] = None
+) -> None:
 
     # Copy platform related files to the suite directory
     # --------------------------------------------------
@@ -256,7 +285,11 @@ def copy_platform_files(logger, exp_suite_path, platform=None):
 # --------------------------------------------------------------------------------------------------
 
 
-def template_modules_file(logger, experiment_dict, exp_suite_path):
+def template_modules_file(
+    logger: Logger,
+    experiment_dict: dict,
+    exp_suite_path: str
+) -> None:
 
     # Modules file
     # ------------
@@ -309,7 +342,10 @@ def template_modules_file(logger, experiment_dict, exp_suite_path):
 # --------------------------------------------------------------------------------------------------
 
 
-def create_modules_csh(logger, exp_suite_path):
+def create_modules_csh(
+    logger: Logger,
+    exp_suite_path: str
+) -> None:
 
     # Modules file
     # ------------
@@ -357,7 +393,13 @@ def create_modules_csh(logger, exp_suite_path):
 # --------------------------------------------------------------------------------------------------
 
 
-def prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experiment_dict, platform):
+def prepare_cylc_suite_jinja2(
+    logger: Logger,
+    swell_suite_path: str,
+    exp_suite_path: str,
+    experiment_dict: dict,
+    platform: str
+) -> None:
 
     # Open suite file from swell
     # --------------------------

src/swell/deployment/launch_experiment.py

@@ -19,7 +19,13 @@
 
 class DeployWorkflow():
 
-    def __init__(self, suite_path, experiment_name, no_detach, log_path):
+    def __init__(
+        self,
+        suite_path: str,
+        experiment_name: str,
+        no_detach: bool,
+        log_path: str
+    ) -> None:
 
         self.logger = Logger('DeployWorkflow')
         self.suite_path = suite_path
@@ -29,7 +35,7 @@ def __init__(self, suite_path, experiment_name, no_detach, log_path):
 
     # ----------------------------------------------------------------------------------------------
 
-    def cylc_run_experiment(self):  # NB: Could be a factory based on workflow_manager
+    def cylc_run_experiment(self) -> None:  # NB: Could be a factory based on workflow_manager
 
         # Move to the suite path
         os.chdir(self.suite_path)
@@ -93,7 +99,11 @@ def cylc_run_experiment(self):  # NB: Could be a factory based on workflow_manag
 # --------------------------------------------------------------------------------------------------
 
 
-def launch_experiment(suite_path, no_detach, log_path):
+def launch_experiment(
+    suite_path: str,
+    no_detach: bool,
+    log_path: str
+) -> None:
 
     # Get the path to where the suite files are located
     # -------------------------------------------------

src/swell/deployment/platforms/platforms.py

@@ -17,15 +17,15 @@
 # --------------------------------------------------------------------------------------------------
 
 
-def platform_path():
+def platform_path() -> str:
 
     return os.path.join(get_swell_path(), 'deployment', 'platforms')
 
 
 # --------------------------------------------------------------------------------------------------
 
 
-def get_platforms():
+def get_platforms() -> list:
 
     # Get list of supported platforms
     platforms = [dir for dir in os.listdir(platform_path())
@@ -41,7 +41,7 @@ def get_platforms():
 # --------------------------------------------------------------------------------------------------
 
 
-def login_or_compute(platform):
+def login_or_compute(platform) -> str:
 
     # Open the properties file
     properties_file = os.path.join(platform_path(), 'properties.yaml')

src/swell/deployment/prepare_config_and_suite/question_and_answer_cli.py

@@ -10,6 +10,7 @@
 
 import re
 import sys
+from typing import Union
 
 import questionary
 from questionary import Choice
@@ -20,7 +21,7 @@
 
 class GetAnswerCli:
 
-    def get_answer(self, key, val):
+    def get_answer(self, key: str, val: dict) -> str:
         # Set questionary variable
         widget_type = val['type']
         quest = val['prompt']
@@ -60,14 +61,14 @@ def get_answer(self, key, val):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_string_widget(self, quest, default, prompt):
+    def make_string_widget(self, quest: str, default: str, prompt: questionary.text) -> str:
         answer = prompt(f"{quest} [{default}]", default=default).ask()
 
         return answer
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_int_widget(self, quest, default, prompt):
+    def make_int_widget(self, quest: str, default: str, prompt: questionary.text) -> str:
         default = str(default)
         answer = prompt(f"{quest} [{default}]",
                         validate=lambda text: True if text.isdigit()
@@ -78,7 +79,12 @@ def make_int_widget(self, quest, default, prompt):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_float_widget(self, quest, default, prompt):
+    def make_float_widget(
+        self,
+        quest: str,
+        default: str,
+        prompt: questionary.text
+    ) -> str:
         default = str(default)
         answer = prompt(f"{quest} [{default}]",
                         validate=lambda text: True if text.isdigit()
@@ -89,7 +95,15 @@ def make_float_widget(self, quest, default, prompt):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_drop_widget(self, method, quest, options, default, prompt):
+    def make_drop_widget(
+        self,
+        method: str,
+        quest: str,
+        options: list,
+        default: str,
+        prompt: questionary.text
+    ) -> Union[str, list]:
+
         default = str(default)
         choices = [str(x) for x in options]
         answer = prompt(quest, choices=choices, default=default).ask()
@@ -98,14 +112,25 @@ def make_drop_widget(self, method, quest, options, default, prompt):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_boolean(self, quest, default, prompt):
+    def make_boolean(
+        self,
+        quest: str,
+        default: str,
+        prompt: questionary.text
+    ) -> bool:
+
         answer = prompt(quest, default=default, auto_enter=False).ask()
 
         return answer
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_datetime(self, quest, default, prompt):
+    def make_datetime(
+        self,
+        quest: str,
+        default: str,
+        prompt: questionary.text
+    ) -> str:
 
         class dtValidator(questionary.Validator):
             def validate(self, document):
@@ -124,7 +149,12 @@ def validate(self, document):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_duration(self, quest, default, prompt):
+    def make_duration(
+        self,
+        quest: str,
+        default: str,
+        prompt: questionary.text
+    ) -> str:
 
         class durValidator(questionary.Validator):
             def validate(self, document):
@@ -157,7 +187,14 @@ def validate(self, document):
 
     # ----------------------------------------------------------------------------------------------
 
-    def make_check_widget(self, quest, options, default, prompt):
+    def make_check_widget(
+        self,
+        quest: str,
+        options: list,
+        default: Union[str, list],
+        prompt: questionary.text
+    ) -> str:
+
         choices = options.copy()
 
         if isinstance(default, list):

src/swell/deployment/prepare_config_and_suite/question_and_answer_defaults.py

@@ -8,9 +8,13 @@
 # --------------------------------------------------------------------------------------------------
 
 
+from typing import Union
+from datetime import datetime as dt
+
+
 class GetAnswerDefaults:
 
-    def get_answer(self, key, val):
+    def get_answer(self, key: str, val: dict) -> Union[int, float, str, dt]:
         return val['default_value']
 
 # --------------------------------------------------------------------------------------------------