Command to create directory structure to run OSeMOSYS_step in desired location

README.md

@@ -171,8 +171,7 @@ in importing coal, importing RL1, and if RLu is allowed to run or not. Add the f
 
 ## 4. Run the workflow
 ```bash
-cd src
-python main_ms.py --step_length 5 --input_data ../data/<datafile_name>.txt
+step run --step_length 5 --input_data ../data/<datafile_name>.txt
 ```
 
 ## 6. View Results

env.yaml

@@ -9,6 +9,7 @@ dependencies:
  - pip
  - pandas
  - snakemake-minimal
+ - glpk>=5.0
  - pip:
       - otoole>=1.0.0
       - click

pyproject.toml

@@ -29,7 +29,8 @@ dependencies = [
   "otoole>=1.1",
   "snakemake",
   "click",
-  "tqdm"
+  "tqdm",
+  "glpk"
   ]
 
 [project.urls]
@@ -38,7 +39,7 @@ Issues = "https://github.com/KTH-dESA/OSeMOSYS_step/issues"
 Source = "https://github.com/KTH-dESA/OSeMOSYS_step"
 
 [project.scripts]
-step = "osemosys_step.main:main"
+step = "osemosys_step.main:cli"
 
 [tool.hatch.version]
 source = "vcs"

src/osemosys_step/main.py

@@ -10,25 +10,34 @@
 """
 
 import click
-from . import data_split as ds
+from osemosys_step import data_split as ds
+from osemosys_step import main_utils as mu
+from osemosys_step import (
+    utils,
+    preprocess_data,
+    solve
+)
 import os
 from pathlib import Path
 import pandas as pd
 import shutil
-from . import utils
-from . import main_utils as mu
-from . import preprocess_data
-from . import solve
 from tqdm import tqdm
 import logging
 import sys
 import glob
-import snakemake 
+import subprocess
 
 from otoole import read, write
 
 logger = logging.getLogger(__name__)
 
+from snakemake.utils import min_version
+min_version("8.0")
+
+@click.group()
+def cli():
+    pass
+
 @click.command()
 @click.option("--step_length", required=True, multiple=True,
               help="""
@@ -52,7 +61,7 @@
               saved elsewhere than '../data/scenarios/' on can use this option to
               indicate the path.
               """)
-def main(input_data: str, step_length: int, path_param: str, cores: int, solver=None, foresight=None):
+def run(input_data: str, step_length: int, path_param: str, cores: int, solver=None, foresight=None):
     """Main entry point for workflow"""
 
     ##########################################################################
@@ -314,13 +323,16 @@ def main(input_data: str, step_length: int, path_param: str, cores: int, solver=
         # when the goal is to just parallize multiple function calls
         #######
 
-        snakemake.snakemake(
-            "src/osemosys_step/snakefile", 
-            config = {"solver":solver, "files":lps_to_solve},
-            cores = cores,
-            keepgoing=True
-        )
-
+        # pretty sure there is a way to directly use the SnakemakeApi class! 
+        snakefile_args = [
+            "--snakefile src/osemosys_step/snakefile", 
+            f"--config solver={solver} files={[','.join(lps_to_solve)]}",
+            f"--cores {cores}",
+            "--keep-going",
+            "--quiet"
+        ]
+        subprocess.run(f"snakemake {' '.join(snakefile_args)}", shell = True)
+
         ######################################################################
         # Check for solutions
         ######################################################################
@@ -621,5 +633,35 @@ def main(input_data: str, step_length: int, path_param: str, cores: int, solver=
 
                     next_step += 1
 
+@click.command()
+@click.option("--path", required=True, default= '.',
+    help="Path where the directory structure shall be created."
+)
+def setup(path: str):
+    """Function to create directory structure in which OSeMOSYS_step can be run.
+    The created directory has the below structure:
+    ```bash
+    OSeMOSYS_step
+    ├── data
+    │   ├── scenarios
+    ├── model
+    ├── results
+    └── steps
+    ```
+    """
+
+    dirs = ['data', ['data', 'scenarios'], 'logs', 'model', 'results', 'steps']
+
+    for d in dirs:
+        if type(d) == list:
+            p = Path(path, *d)
+        else:
+            p = Path(path, d)
+        if not p.exists():
+            p.mkdir()
+
+cli.add_command(run)
+cli.add_command(setup)
+
 if __name__ == '__main__':
-    main() #input_data,step_length,path_param,solver)
+    cli()

src/osemosys_step/snakefile

@@ -1,5 +1,8 @@
 
-options = [x[12:-9] for x in config["files"]] # extract out only the option path
+if isinstance(config["files"], str):
+    options = [config["files"][12:-9]]
+else:
+    options = [x[12:-9] for x in config["files"]] # extract out only the option path
 
 rule all:
     input: