Apply black formatter

Apply black formatter to python files touched in the rebase. Took the
simple approach of just accepting the `dev` changes always, which were
not linted.

examples/test_cli.py

@@ -74,9 +74,7 @@ def test_sample_2pop_modifiers_combined_deprecated():
 def test_simple_usa_statelevel_deprecated():
     os.chdir(os.path.dirname(__file__) + "/simple_usa_statelevel")
     runner = CliRunner()
-    result = runner.invoke(
-        _click_simulate, ["-n", "1", "-c", "simple_usa_statelevel.yml"]
-    )
+    result = runner.invoke(_click_simulate, ["-n", "1", "-c", "simple_usa_statelevel.yml"])
     print(result.output)  # useful for debug
     print(result.exit_code)  # useful for debug
     print(result.exception)  # useful for debug

flepimop/gempyor_pkg/src/gempyor/cli.py

@@ -22,10 +22,11 @@
 # add some basic commands to the CLI
 @cli.command(params=[config_files_argument] + list(config_file_options.values()))
 @pass_context
-def patch(ctx : Context = mock_context, **kwargs) -> None:
+def patch(ctx: Context = mock_context, **kwargs) -> None:
     """Merge configuration files"""
     parse_config_files(config, ctx, **kwargs)
     print(config.dump())
 
+
 if __name__ == "__main__":
     cli()

flepimop/gempyor_pkg/src/gempyor/compartments.py

@@ -892,20 +892,24 @@ def list_recursive_convert_to_string(thing):
         return [list_recursive_convert_to_string(x) for x in thing]
     return str(thing)
 
+
 @cli.group()
 @pass_context
 def compartments(ctx: Context):
     """Commands for working with FlepiMoP compartments"""
     pass
 
+
 @compartments.command(params=[config_files_argument] + list(config_file_options.values()))
 @pass_context
-def plot(ctx : Context, **kwargs):
+def plot(ctx: Context, **kwargs):
     """Plot compartments"""
     parse_config_files(config, ctx, **kwargs)
     assert config["compartments"].exists()
     assert config["seir"].exists()
-    comp = Compartments(seir_config=config["seir"], compartments_config=config["compartments"])
+    comp = Compartments(
+        seir_config=config["seir"], compartments_config=config["compartments"]
+    )
 
     # TODO: this should be a command like build compartments.
     (
@@ -920,12 +924,14 @@ def plot(ctx : Context, **kwargs):
 
 @compartments.command(params=[config_files_argument] + list(config_file_options.values()))
 @pass_context
-def export(ctx : Context, **kwargs):
+def export(ctx: Context, **kwargs):
     """Export compartments"""
     parse_config_files(config, ctx, **kwargs)
     assert config["compartments"].exists()
     assert config["seir"].exists()
-    comp = Compartments(seir_config=config["seir"], compartments_config=config["compartments"])
+    comp = Compartments(
+        seir_config=config["seir"], compartments_config=config["compartments"]
+    )
     (
         unique_strings,
         transition_array,
@@ -935,4 +941,5 @@ def export(ctx : Context, **kwargs):
     comp.toFile("compartments_file.csv", "transitions_file.csv", write_parquet=False)
     print("wrote files 'compartments_file.csv', 'transitions_file.csv' ")
 
-cli.add_command(compartments)
+
+cli.add_command(compartments)

flepimop/gempyor_pkg/src/gempyor/config_validator.py

@@ -12,6 +12,7 @@
 from functools import partial
 from gempyor import compartments
 
+
 def read_yaml(file_path: str) -> dict:
     with open(file_path, "r") as stream:
         config = yaml.safe_load(stream)
@@ -23,11 +24,13 @@ def allowed_values(v, values):
     assert v in values
     return v
 
+
 # def parse_value(cls, values):
 #     value = values.get('value')
 #     parsed_val = compartments.Compartments.parse_parameter_strings_to_numpy_arrays_v2(value)
 #     return parsed_val
-
+
+
 class SubpopSetupConfig(BaseModel):
     geodata: str
     mobility: Optional[str]

flepimop/gempyor_pkg/src/gempyor/shared_cli.py

@@ -23,6 +23,7 @@ def cli(ctx: click.Context) -> None:
     """Flexible Epidemic Modeling Platform (FlepiMoP) Command Line Interface"""
     pass
 
+
 # click decorator to handle configuration file(s) as arguments
 # use as `@argument_config_files` before a cli command definition
 config_files_argument = click.Argument(
@@ -162,9 +163,7 @@ def decorator(func: Callable[..., Any]) -> Callable[..., Any]:
         additional_doc = "\n\tCommand Line Interface arguments:\n"
         for param in params:
             paraminfo = param.to_info_dict()
-            additional_doc += (
-                f"\n\t{paraminfo['name']}: {paraminfo['type']['param_type']}"
-            )
+            additional_doc += f"\n\t{paraminfo['name']}: {paraminfo['type']['param_type']}"
 
         if func.__doc__ is None:
             func.__doc__ = ""
@@ -203,9 +202,7 @@ def parse_config_files(
 
     def _parse_option(param: click.Parameter, value: Any) -> Any:
         """internal parser to autobox values"""
-        if (param.multiple or param.nargs == -1) and not isinstance(
-            value, (list, tuple)
-        ):
+        if (param.multiple or param.nargs == -1) and not isinstance(value, (list, tuple)):
             value = [value]
         return param.type_cast_value(ctx, value)
 
@@ -244,9 +241,7 @@ def _parse_option(param: click.Parameter, value: Any) -> Any:
             tmp = confuse.Configuration("tmp")
             tmp.set_file(config_file)
             if intersect := set(tmp.keys()) & set(cfg.keys()):
-                warnings.warn(
-                    f"Configuration files contain overlapping keys: {intersect}."
-                )
+                warnings.warn(f"Configuration files contain overlapping keys: {intersect}.")
             cfg.set_file(config_file)
         cfg["config_src"] = [str(k) for k in config_src]
 
@@ -268,5 +263,5 @@ def _parse_option(param: click.Parameter, value: Any) -> Any:
         if (value := kwargs.get(option)) is not None:
             # auto box the value if the option expects a multiple
             cfg[option] = _parse_option(config_file_options[option], value)
-    
+
     return cfg

flepimop/gempyor_pkg/src/gempyor/simulate.py

@@ -165,10 +165,18 @@
 from click import Context, pass_context
 
 from . import seir, outcomes, model_info, utils
-from .shared_cli import config_files_argument, config_file_options, parse_config_files, cli, click_helpstring, mock_context
+from .shared_cli import (
+    config_files_argument,
+    config_file_options,
+    parse_config_files,
+    cli,
+    click_helpstring,
+    mock_context,
+)
 
 # from .profile import profile_options
 
+
 # @profile_options
 # @profile()
 def simulate(
@@ -184,7 +192,7 @@ def simulate(
     write_parquet: bool = True,
     first_sim_index: int = 1,
     stoch_traj_flag: bool = False,
-    verbose : bool = True,
+    verbose: bool = True,
 ) -> int:
     """
     Forward simulate a model using gempyor.
@@ -216,14 +224,26 @@ def simulate(
         cfg = config_filepath
 
     scenarios_combinations = [
-        [s, d] for s in (cfg["seir_modifiers"]["scenarios"].as_str_seq() if cfg["seir_modifiers"].exists() else [None])
-        for d in (cfg["outcome_modifiers"]["scenarios"].as_str_seq() if cfg["outcome_modifiers"].exists() else [None])]
-
+        [s, d]
+        for s in (
+            cfg["seir_modifiers"]["scenarios"].as_str_seq()
+            if cfg["seir_modifiers"].exists()
+            else [None]
+        )
+        for d in (
+            cfg["outcome_modifiers"]["scenarios"].as_str_seq()
+            if cfg["outcome_modifiers"].exists()
+            else [None]
+        )
+    ]
+
     if verbose:
         print("Combination of modifiers scenarios to be run: ")
         print(scenarios_combinations)
         for seir_modifiers_scenario, outcome_modifiers_scenario in scenarios_combinations:
-            print(f"seir_modifier: {seir_modifiers_scenario}, outcomes_modifier: {outcome_modifiers_scenario}")
+            print(
+                f"seir_modifier: {seir_modifiers_scenario}, outcomes_modifier: {outcome_modifiers_scenario}"
+            )
 
     nchains = cfg["nslots"].as_number()
 
@@ -265,17 +285,25 @@ def simulate(
         if cfg["seir"].exists():
             seir.run_parallel_SEIR(modinf, config=cfg, n_jobs=cfg["jobs"].get(int))
         if cfg["outcomes"].exists():
-            outcomes.run_parallel_outcomes(sim_id2write=cfg["first_sim_index"].get(int), modinf=modinf, nslots=nchains, n_jobs=cfg["jobs"].get(int))
+            outcomes.run_parallel_outcomes(
+                sim_id2write=cfg["first_sim_index"].get(int),
+                modinf=modinf,
+                nslots=nchains,
+                n_jobs=cfg["jobs"].get(int),
+            )
         if verbose:
             print(
                 f">>> {seir_modifiers_scenario}_{outcome_modifiers_scenario} completed in {time.monotonic() - start:.1f} seconds"
             )
 
     return 0
 
-@cli.command(name="simulate", params=[config_files_argument] + list(config_file_options.values()))
+
+@cli.command(
+    name="simulate", params=[config_files_argument] + list(config_file_options.values())
+)
 @pass_context
-def _click_simulate(ctx : Context, **kwargs) -> int:
+def _click_simulate(ctx: Context, **kwargs) -> int:
     """Forward simulate a model using gempyor."""
     cfg = parse_config_files(utils.config, ctx, **kwargs)
     return simulate(cfg)
@@ -285,16 +313,20 @@ def _click_simulate(ctx : Context, **kwargs) -> int:
 
 import subprocess
 
-def _deprecated_simulate(argv : list[str] = []) -> int:
+
+def _deprecated_simulate(argv: list[str] = []) -> int:
     if not argv:
         argv = sys.argv[1:]
-    clickcmd = ' '.join(['flepimop', 'simulate'] + argv)
-    warnings.warn(f"This command is deprecated, use the CLI instead: `{clickcmd}`", DeprecationWarning)
+    clickcmd = " ".join(["flepimop", "simulate"] + argv)
+    warnings.warn(
+        f"This command is deprecated, use the CLI instead: `{clickcmd}`", DeprecationWarning
+    )
     return subprocess.run(clickcmd, shell=True).returncode
 
+
 if __name__ == "__main__":
     argv = sys.argv[1:]
-    clickcmd = ' '.join(['flepimop', 'simulate'] + argv)
+    clickcmd = " ".join(["flepimop", "simulate"] + argv)
     warnings.warn(f"Use the CLI instead: `{clickcmd}`", DeprecationWarning)
     _deprecated_simulate(argv)
 

flepimop/gempyor_pkg/src/gempyor/testing.py

@@ -57,6 +57,7 @@ def mock_empty_config() -> confuse.Configuration:
     """
     return confuse.Configuration("flepiMoPMock", read=False)
 
+
 def create_confuse_config_from_file(
     data_file: Path,
 ) -> confuse.Configuration:
@@ -74,6 +75,7 @@ def create_confuse_config_from_file(
     cv.set_file(data_file)
     return cv
 
+
 def create_confuse_configview_from_dict(
     data: dict[str, Any], name: None | str = None
 ) -> confuse.ConfigView:
@@ -133,9 +135,8 @@ def create_confuse_configview_from_dict(
     cv = cv[name] if name is not None else cv
     return cv
 
-def create_confuse_config_from_dict(
-    data: dict[str, Any]
-) -> confuse.Configuration:
+
+def create_confuse_config_from_dict(data: dict[str, Any]) -> confuse.Configuration:
     """
     Create a Configuration from a dictionary for unit testing confuse parameters.
 

flepimop/gempyor_pkg/tests/shared_cli/test_cli.py

@@ -21,6 +21,7 @@ def test_config_sample_2pop():
     result = runner.invoke(_click_simulate, ["config_sample_2pop.yml"])
     assert result.exit_code == 0
 
+
 def test_config_sample_2pop_deprecated():
     os.chdir(tutorialpath)
     runner = CliRunner()
@@ -42,29 +43,36 @@ def test_sample_2pop_modifiers():
     assert result.exit_code == 0
 
 
-def test_sample_2pop_modifiers_combined(tmp_path : Path):
+def test_sample_2pop_modifiers_combined(tmp_path: Path):
     os.chdir(tutorialpath)
     tmp_cfg1 = tmp_path / "patch_modifiers.yml"
     tmp_cfg2 = tmp_path / "nopatch_modifiers.yml"
     runner = CliRunner()
-
-    result = runner.invoke(patch, ["config_sample_2pop.yml",
+
+    result = runner.invoke(
+        patch,
+        [
+            "config_sample_2pop.yml",
             "config_sample_2pop_outcomes_part.yml",
-            "config_sample_2pop_modifiers_part.yml"])
+            "config_sample_2pop_modifiers_part.yml",
+        ],
+    )
     assert result.exit_code == 0
     with open(tmp_cfg1, "w") as f:
         f.write(result.output)
-    
+
     result = runner.invoke(patch, ["config_sample_2pop_modifiers.yml"])
     assert result.exit_code == 0
     with open(tmp_cfg2, "w") as f:
         f.write(result.output)
-
-
+
     tmpconfig1 = create_confuse_config_from_file(str(tmp_cfg1)).flatten()
     tmpconfig2 = create_confuse_config_from_file(str(tmp_cfg2)).flatten()
 
-    assert { k: v for k, v in tmpconfig1.items() if k != "config_src" } == { k: v for k, v in tmpconfig2.items() if k != "config_src" }
+    assert {k: v for k, v in tmpconfig1.items() if k != "config_src"} == {
+        k: v for k, v in tmpconfig2.items() if k != "config_src"
+    }
+
 
 def test_simple_usa_statelevel_more_deprecated():
     os.chdir(tutorialpath + "/../simple_usa_statelevel")

flepimop/gempyor_pkg/tests/shared_cli/test_parse_config_files.py

@@ -1,4 +1,3 @@
-
 import pathlib
 from typing import Any
 
@@ -159,7 +158,7 @@ def test_multifile_config_collision(
         tmpconfigfile1 = config_file(tmp_path, testdict1, "config1.yaml")
         tmpconfigfile2 = config_file(tmp_path, testdict2, "config2.yaml")
         mockconfig = mock_empty_config()
-        with pytest.warns(UserWarning, match=r'foo'):
+        with pytest.warns(UserWarning, match=r"foo"):
             parse_config_files(mockconfig, config_files=[tmpconfigfile1, tmpconfigfile2])
         for k, v in (testdict1 | testdict2).items():
             assert mockconfig[k].get(v) == v