feat!: addition of proper logging functionality for the ViroConstrict…

…or package

feat!: replace snakemake logging output through our own log handler for unified output

fix: suppress snakemake logging output (workaround for snakemake/snakemake#2089)

refactor!: Use a generic (`__main__.py`) top level entry-point instead of the named `ViroConstrictor.py` entrypoint

refactor: re-structure argument parsing functionalities into its own class

refactor: re-structure snakemake run-information and config functionalities into its own class

refactor: remove old shell stdout-coloring method with the rich library

refactor: simplify several functions to ensure a properly defined return

refactor: Use f-strings more consistently for i.e. string concatenation with variables

refactor: add type-hints to all functions

fix: ensure `samples_df` and `samples_dict` always contain the same information

ViroConstrictor/__main__.py

@@ -0,0 +1,192 @@
+"""
+Starting point of the ViroConstrictor pipeline and wrapper
+
+Copyright © 2021 RIVM
+
+https://github.com/RIVM-bioinformatics/ViroConstrictor
+"""
+
+# pylint: disable=C0103
+
+import sys
+from typing import Literal, NoReturn
+
+import pandas as pd
+import snakemake
+
+import ViroConstrictor.logging
+from ViroConstrictor import __version__
+from ViroConstrictor.logging import log
+from ViroConstrictor.parser import CLIparser
+from ViroConstrictor.runconfigs import GetSnakemakeRunDetails, WriteYaml
+from ViroConstrictor.runreport import WriteReport
+from ViroConstrictor.update import update
+
+
+def get_preset_warning_list(
+    sample_info_df: pd.DataFrame,
+) -> tuple[list[str], list[str]]:
+    """Takes a dataframe with sample information and returns a tuple of two lists of warnings
+
+    Parameters
+    ----------
+    sample_info_df : pd.DataFrame
+        pd.DataFrame
+
+    Returns
+    -------
+        A list of warnings.
+
+    """
+    preset_fallback_warnings = preset_score_warnings = []
+    for s in sample_info_df.itertuples():
+        sample, preset, score, input_target = (
+            s.SAMPLE,
+            s.PRESET,
+            s.PRESET_SCORE,
+            s.VIRUS,
+        )
+        if score == 0.0:
+            warn = f"""[red]Sample '[bold underline]{sample}[/bold underline]' was given the following information as an input-target: '[bold underline]{input_target}[/bold underline]'.
+This information could however not be used to determine a preset. Because of this, the preset '[bold underline]{preset}[/bold underline]' was used instead.[/red]
+[yellow]Please check your input-target for any significant misspellings, or consider using an alias or a different abbreviation for your input-target to check whether this resolves the issue.[/yellow]
+
+It may be that your input-target does not yet have an associated preset in ViroConstrictor. 
+If your suspect this to be the case, please open an issue on the ViroConstrictor GitHub page: [magenta underline]https://github.com/RIVM-bioinformatics/ViroConstrictor[/magenta underline]"""
+            preset_fallback_warnings.append(warn)
+            continue
+        if score < 0.8:
+            warn = f"""[red]Sample '[bold underline]{sample}[/bold underline]' was given the following information as an input-target: '[bold underline]{input_target}[/bold underline]'.
+As a result, the preset '{preset}' was chosen. But this was done with less than 80% certainty.[/red]
+[yellow]Certainty score: [bold]{score:.0%}[/bold][/yellow]
+Please check the input-target and try again if a different preset is required."""
+            preset_score_warnings.append(warn)
+            continue
+    return preset_fallback_warnings, preset_score_warnings
+
+
+def show_preset_warnings(
+    warnings: list[str], fallbacks: list[str], disabled: bool
+) -> None:
+    if warnings and not disabled:
+        for w in warnings:
+            log.warn(f"{w}")
+    if fallbacks and not disabled:
+        for w in fallbacks:
+            log.warn(f"{w}")
+
+
+def main() -> NoReturn:
+    """
+    ViroConstrictor starting point
+    --> Fetch and parse arguments
+    --> check validity
+    --> Read (or write, if necessary) the user-config files
+    --> Change working directories and make necessary local files for snakemake
+    --> Run snakemake with appropriate settings
+    """
+
+    parsed_input = CLIparser(input_args=sys.argv[1:])
+
+    preset_fallback_warnings, preset_score_warnings = get_preset_warning_list(
+        parsed_input.samples_df
+    )
+    if not parsed_input.flags.skip_updates:
+        update(sys.argv, parsed_input.user_config)
+
+    snakemake_run_details = GetSnakemakeRunDetails(inputs_obj=parsed_input)
+
+    log.info(f"{'='*20} [bold yellow] Starting Workflow [/bold yellow] {'='*20}")
+    status: bool = False
+
+    if parsed_input.user_config["COMPUTING"]["compmode"] == "local":
+        status = snakemake.snakemake(
+            snakefile=parsed_input.snakefile,
+            workdir=parsed_input.workdir,
+            cores=snakemake_run_details.snakemake_run_conf["cores"],
+            use_conda=snakemake_run_details.snakemake_run_conf["use-conda"],
+            conda_frontend="mamba",
+            jobname=snakemake_run_details.snakemake_run_conf["jobname"],
+            latency_wait=snakemake_run_details.snakemake_run_conf["latency-wait"],
+            dryrun=snakemake_run_details.snakemake_run_conf["dryrun"],
+            configfiles=[
+                WriteYaml(
+                    snakemake_run_details.snakemake_run_parameters,
+                    f"{parsed_input.workdir}/config/run_params.yaml",
+                )
+            ],
+            restart_times=3,
+            keepgoing=True,
+            quiet=["all"],  # type: ignore
+            log_handler=[
+                ViroConstrictor.logging.snakemake_logger(logfile=parsed_input.logfile)
+            ],
+            printshellcmds=False,
+        )
+    if parsed_input.user_config["COMPUTING"]["compmode"] == "grid":
+        status = snakemake.snakemake(
+            snakefile=parsed_input.snakefile,
+            workdir=parsed_input.workdir,
+            cores=snakemake_run_details.snakemake_run_conf["cores"],
+            nodes=snakemake_run_details.snakemake_run_conf["cores"],
+            use_conda=snakemake_run_details.snakemake_run_conf["use-conda"],
+            conda_frontend="mamba",
+            jobname=snakemake_run_details.snakemake_run_conf["jobname"],
+            latency_wait=snakemake_run_details.snakemake_run_conf["latency-wait"],
+            drmaa=snakemake_run_details.snakemake_run_conf["drmaa"],
+            drmaa_log_dir=snakemake_run_details.snakemake_run_conf["drmaa-log-dir"],
+            dryrun=snakemake_run_details.snakemake_run_conf["dryrun"],
+            configfiles=[
+                WriteYaml(
+                    snakemake_run_details.snakemake_run_parameters,
+                    f"{parsed_input.workdir}/config/run_params.yaml",
+                )
+            ],
+            restart_times=3,
+            keepgoing=True,
+            quiet=["all"],  # type: ignore
+            log_handler=[
+                ViroConstrictor.logging.snakemake_logger(logfile=parsed_input.logfile)
+            ],
+        )
+
+    if snakemake_run_details.snakemake_run_conf["dryrun"] is False and status is True:
+        snakemake.snakemake(
+            snakefile=parsed_input.snakefile,
+            workdir=parsed_input.workdir,
+            report="results/snakemake_report.html",
+            configfiles=[
+                WriteYaml(
+                    snakemake_run_details.snakemake_run_parameters,
+                    f"{parsed_input.workdir}/config/run_params.yaml",
+                )
+            ],
+            quiet=["all"],  # type: ignore
+            log_handler=[
+                ViroConstrictor.logging.snakemake_logger(logfile=parsed_input.logfile)
+            ],
+        )
+
+    workflow_state: Literal["Failed", "Success"] = (
+        "Failed" if status is False else "Success"
+    )
+
+    WriteReport(
+        parsed_input.workdir,
+        parsed_input.input_path,
+        parsed_input.exec_start_path,
+        parsed_input.user_config,
+        snakemake_run_details.snakemake_run_parameters,
+        snakemake_run_details.snakemake_run_conf,
+        workflow_state,
+    )
+
+    show_preset_warnings(
+        preset_score_warnings,
+        preset_fallback_warnings,
+        parsed_input.flags.disable_presets,
+    )
+
+    if status is False:
+        exit(1)
+    exit(0)