From 029892fae2d058c98ab02b0562a44cba2a15c7df Mon Sep 17 00:00:00 2001
From: Zach Smith <zachsmith.sa@gmail.com>
Date: Wed, 12 Apr 2023 16:31:21 +0200
Subject: [PATCH] Refactored CLI layout to be more intuitive in terms of
 naming, and also the module logic is no longer imported into weird places
 before executing (#30)

---
 toolkit/__main__.py                           | 77 +++++++++++--------
 toolkit/cli/__init__.py                       |  4 +-
 toolkit/cli/applications/__init__.py          |  3 +
 toolkit/cli/applications/kerchunk/__init__.py |  3 +
 .../kerchunk/run/__init__.py                  |  0
 .../lacce/__init__.py                         |  0
 toolkit/cli/applications/mhw/__init__.py      |  4 +
 .../mhw/start/__init__.py                     |  3 +-
 .../mhw/thresholds/__init__.py                |  6 +-
 .../mhw/thresholds/catalogue/__init__.py      |  3 +
 .../mhw/thresholds/catalogue/update_cache.py  |  0
 .../mhw/thresholds/climatology/__init__.py    |  4 +
 .../mhw/thresholds/climatology/daily.py       |  0
 .../mhw/thresholds/climatology/define_mhw.py  |  0
 toolkit/cli/applications/ops/__init__.py      |  5 ++
 .../ops/download/__init__.py                  |  4 +-
 .../ops/download/gfs/__init__.py              |  2 +-
 .../ops/download/gfs/functions.py             |  0
 .../ops/download/mercator/__init__.py         |  0
 .../ops/load/__init__.py                      |  9 ++-
 .../ops/load/coordinates/__init__.py          |  0
 .../ops/load/coordinates/coordinates.sql      |  0
 .../ops/load/finalize/__init__.py             |  0
 .../ops/load/models.yml                       |  0
 .../ops/load/raster2pgsql/__init__.py         |  0
 .../raster2pgsql/update-raster_xref_run.sql   |  0
 .../ops/load/values/__init__.py               |  2 +-
 .../ops/load/values/load_band.py              |  0
 .../ops/transform/__init__.py                 |  4 +-
 .../ops/transform/depth_functions.py          |  0
 .../ops/transform/functions.py                |  0
 .../update/__init__.py                        |  0
 .../update/update_bashrc.py                   |  0
 toolkit/cli/commands/__init__.py              |  3 -
 toolkit/cli/define/__init__.py                |  3 +
 .../{commands => define}/kerchunk/__init__.py |  0
 .../{commands => define}/lacce/__init__.py    |  0
 .../cli/{commands => define}/mhw/__init__.py  |  0
 .../cli/{commands => define}/ops/__init__.py  |  0
 .../{commands => define}/update/__init__.py   |  0
 toolkit/cli/exe/kerchunk/__init__.py          |  7 --
 toolkit/cli/exe/mhw/__init__.py               |  7 --
 toolkit/cli/modules/__init__.py               |  3 -
 toolkit/cli/modules/kerchunk/__init__.py      |  3 -
 toolkit/cli/modules/mhw/__init__.py           |  4 -
 .../mhw/thresholds/catalogue/__init__.py      |  3 -
 .../mhw/thresholds/climatology/__init__.py    |  4 -
 toolkit/cli/modules/ops/__init__.py           |  5 --
 toolkit/cli/{exe => parse}/__init__.py        |  2 +-
 toolkit/cli/parse/kerchunk/__init__.py        |  5 ++
 toolkit/cli/{exe => parse}/lacce/__init__.py  |  4 +-
 toolkit/cli/parse/mhw/__init__.py             |  5 ++
 toolkit/cli/{exe => parse}/ops/__init__.py    | 11 +--
 toolkit/cli/{exe => parse}/update/__init__.py |  9 +--
 54 files changed, 108 insertions(+), 103 deletions(-)
 create mode 100644 toolkit/cli/applications/__init__.py
 create mode 100644 toolkit/cli/applications/kerchunk/__init__.py
 rename toolkit/cli/{modules => applications}/kerchunk/run/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/lacce/__init__.py (100%)
 create mode 100644 toolkit/cli/applications/mhw/__init__.py
 rename toolkit/cli/{modules => applications}/mhw/start/__init__.py (52%)
 rename toolkit/cli/{modules => applications}/mhw/thresholds/__init__.py (87%)
 create mode 100644 toolkit/cli/applications/mhw/thresholds/catalogue/__init__.py
 rename toolkit/cli/{modules => applications}/mhw/thresholds/catalogue/update_cache.py (100%)
 create mode 100644 toolkit/cli/applications/mhw/thresholds/climatology/__init__.py
 rename toolkit/cli/{modules => applications}/mhw/thresholds/climatology/daily.py (100%)
 rename toolkit/cli/{modules => applications}/mhw/thresholds/climatology/define_mhw.py (100%)
 create mode 100644 toolkit/cli/applications/ops/__init__.py
 rename toolkit/cli/{modules => applications}/ops/download/__init__.py (91%)
 rename toolkit/cli/{modules => applications}/ops/download/gfs/__init__.py (98%)
 rename toolkit/cli/{modules => applications}/ops/download/gfs/functions.py (100%)
 rename toolkit/cli/{modules => applications}/ops/download/mercator/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/ops/load/__init__.py (94%)
 rename toolkit/cli/{modules => applications}/ops/load/coordinates/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/ops/load/coordinates/coordinates.sql (100%)
 rename toolkit/cli/{modules => applications}/ops/load/finalize/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/ops/load/models.yml (100%)
 rename toolkit/cli/{modules => applications}/ops/load/raster2pgsql/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/ops/load/raster2pgsql/update-raster_xref_run.sql (100%)
 rename toolkit/cli/{modules => applications}/ops/load/values/__init__.py (83%)
 rename toolkit/cli/{modules => applications}/ops/load/values/load_band.py (100%)
 rename toolkit/cli/{modules => applications}/ops/transform/__init__.py (98%)
 rename toolkit/cli/{modules => applications}/ops/transform/depth_functions.py (100%)
 rename toolkit/cli/{modules => applications}/ops/transform/functions.py (100%)
 rename toolkit/cli/{modules => applications}/update/__init__.py (100%)
 rename toolkit/cli/{modules => applications}/update/update_bashrc.py (100%)
 delete mode 100644 toolkit/cli/commands/__init__.py
 create mode 100644 toolkit/cli/define/__init__.py
 rename toolkit/cli/{commands => define}/kerchunk/__init__.py (100%)
 rename toolkit/cli/{commands => define}/lacce/__init__.py (100%)
 rename toolkit/cli/{commands => define}/mhw/__init__.py (100%)
 rename toolkit/cli/{commands => define}/ops/__init__.py (100%)
 rename toolkit/cli/{commands => define}/update/__init__.py (100%)
 delete mode 100644 toolkit/cli/exe/kerchunk/__init__.py
 delete mode 100644 toolkit/cli/exe/mhw/__init__.py
 delete mode 100644 toolkit/cli/modules/__init__.py
 delete mode 100644 toolkit/cli/modules/kerchunk/__init__.py
 delete mode 100644 toolkit/cli/modules/mhw/__init__.py
 delete mode 100644 toolkit/cli/modules/mhw/thresholds/catalogue/__init__.py
 delete mode 100644 toolkit/cli/modules/mhw/thresholds/climatology/__init__.py
 delete mode 100644 toolkit/cli/modules/ops/__init__.py
 rename toolkit/cli/{exe => parse}/__init__.py (50%)
 create mode 100644 toolkit/cli/parse/kerchunk/__init__.py
 rename toolkit/cli/{exe => parse}/lacce/__init__.py (64%)
 create mode 100644 toolkit/cli/parse/mhw/__init__.py
 rename toolkit/cli/{exe => parse}/ops/__init__.py (53%)
 rename toolkit/cli/{exe => parse}/update/__init__.py (61%)

diff --git a/toolkit/__main__.py b/toolkit/__main__.py
index 191add07..142a2714 100644
--- a/toolkit/__main__.py
+++ b/toolkit/__main__.py
@@ -1,18 +1,25 @@
 import argparse
 import os
-from cli.commands import (
-    lacce as lacce_cmd,
-    mhw as mhw_cmd,
-    ops as ops_cmd,
-    kerchunk as kerchunk_cmd,
-    update as update_cmd,
+from cli.define import (
+    lacce as define_lacce,
+    mhw as define_mhw,
+    ops as define_ops,
+    kerchunk as define_kerchunk,
+    update as define_update,
 )
-from cli.exe import (
-    lacce as lacce_exe,
-    mhw as mhw_exe,
-    ops as ops_exe,
-    kerchunk as kerchunk_exe,
-    update as update_exe,
+from cli.parse import (
+    lacce as parse_lacce,
+    mhw as parse_mhw,
+    ops as parse_ops,
+    kerchunk as parse_kerchunk,
+    update as parse_update,
+)
+from cli.applications import (
+    lacce,
+    mhw,
+    ops,
+    kerchunk,
+    update,
 )
 
 prog = "somisana"
@@ -30,29 +37,37 @@ def main():
         metavar="Applications",
     )
 
-    # Build commands
-    mhw = mhw_cmd.build(module_parser)
-    ops = ops_cmd.build(module_parser)
-    lacce = lacce_cmd.build(module_parser)
-    kerchunk = kerchunk_cmd.build(module_parser)
-    update = update_cmd.build(module_parser)
+    # (1) Build commands
+    mhw_app = define_mhw.build(module_parser)
+    ops_app = define_ops.build(module_parser)
+    lacce_app = define_lacce.build(module_parser)
+    kerchunk_app = define_kerchunk.build(module_parser)
+    update_app = define_update.build(module_parser)
 
-    # Parse args
+    # (2) Parse command string
     args = parser.parse_args()
 
-    # Run the CLI
-    if args.command == "ops":
-        ops_exe.run(ops, args)
-    elif args.command == "mhw":
-        mhw_exe.run(mhw, args)
-    elif args.command == "lacce":
-        lacce_exe.run(lacce, args)
-    elif args.command == "kerchunk":
-        kerchunk_exe.run(kerchunk, args)
-    elif args.command == "update":
-        update_exe.run(update, args)
-    else:
+    # (3) Select the application by parsing flag options
+    exe = (
+        parse_ops.parse(ops_app, args, ops)
+        if args.command == "ops"
+        else parse_mhw.parse(mhw_app, args, mhw)
+        if args.command == "mhw"
+        else parse_lacce.parse(lacce_app, args, lacce)
+        if args.command == "lacce"
+        else parse_kerchunk.parse(kerchunk_app, args, kerchunk)
+        if args.command == "kerchunk"
+        else parse_update.run(update_app, args, update)
+        if args.command == "update"
+        else None
+    )
+
+    # (4) Execute the application
+    if not exe:
         parser.print_help()
+        return
+    else:
+        exe(args)
 
 
 if __name__ == "__main__":
diff --git a/toolkit/cli/__init__.py b/toolkit/cli/__init__.py
index 1a91c534..caefeae6 100644
--- a/toolkit/cli/__init__.py
+++ b/toolkit/cli/__init__.py
@@ -1,3 +1,3 @@
-from cli import commands, modules, exe
+from cli import define, applications, parse
 
-__all__ = ["commands", "modules", "exe"]
+__all__ = ["define", "applications", "parse"]
diff --git a/toolkit/cli/applications/__init__.py b/toolkit/cli/applications/__init__.py
new file mode 100644
index 00000000..cf9a880f
--- /dev/null
+++ b/toolkit/cli/applications/__init__.py
@@ -0,0 +1,3 @@
+from cli.applications import lacce, mhw, ops, kerchunk, update
+
+__all__ = ["lacce", "mhw", "ops", "kerchunk", "update"]
diff --git a/toolkit/cli/applications/kerchunk/__init__.py b/toolkit/cli/applications/kerchunk/__init__.py
new file mode 100644
index 00000000..61749244
--- /dev/null
+++ b/toolkit/cli/applications/kerchunk/__init__.py
@@ -0,0 +1,3 @@
+from cli.applications.kerchunk.run import run
+
+__all__ = ["run"]
diff --git a/toolkit/cli/modules/kerchunk/run/__init__.py b/toolkit/cli/applications/kerchunk/run/__init__.py
similarity index 100%
rename from toolkit/cli/modules/kerchunk/run/__init__.py
rename to toolkit/cli/applications/kerchunk/run/__init__.py
diff --git a/toolkit/cli/modules/lacce/__init__.py b/toolkit/cli/applications/lacce/__init__.py
similarity index 100%
rename from toolkit/cli/modules/lacce/__init__.py
rename to toolkit/cli/applications/lacce/__init__.py
diff --git a/toolkit/cli/applications/mhw/__init__.py b/toolkit/cli/applications/mhw/__init__.py
new file mode 100644
index 00000000..645e902f
--- /dev/null
+++ b/toolkit/cli/applications/mhw/__init__.py
@@ -0,0 +1,4 @@
+from cli.applications.mhw.start import start
+from cli.applications.mhw.thresholds import create_thresholds
+
+__all__ = ["start", "create_thresholds"]
diff --git a/toolkit/cli/modules/mhw/start/__init__.py b/toolkit/cli/applications/mhw/start/__init__.py
similarity index 52%
rename from toolkit/cli/modules/mhw/start/__init__.py
rename to toolkit/cli/applications/mhw/start/__init__.py
index 20ee3966..8147320f 100644
--- a/toolkit/cli/modules/mhw/start/__init__.py
+++ b/toolkit/cli/applications/mhw/start/__init__.py
@@ -1,4 +1,5 @@
-from cli.modules.mhw.thresholds import create_thresholds
+from cli.applications.mhw.thresholds import create_thresholds
+
 
 def start(args):
     create_thresholds(args)
diff --git a/toolkit/cli/modules/mhw/thresholds/__init__.py b/toolkit/cli/applications/mhw/thresholds/__init__.py
similarity index 87%
rename from toolkit/cli/modules/mhw/thresholds/__init__.py
rename to toolkit/cli/applications/mhw/thresholds/__init__.py
index 7e25a643..af42ad74 100644
--- a/toolkit/cli/modules/mhw/thresholds/__init__.py
+++ b/toolkit/cli/applications/mhw/thresholds/__init__.py
@@ -1,9 +1,9 @@
 import os
 from os.path import join
 from config import CACHDIR
-from cli.modules.mhw.thresholds.catalogue import update_cache
-from cli.modules.mhw.thresholds.climatology import calculate_daily_clim
-from cli.modules.mhw.thresholds.climatology import calculate_mhw
+from cli.applications.mhw.thresholds.catalogue import update_cache
+from cli.applications.mhw.thresholds.climatology import calculate_daily_clim
+from cli.applications.mhw.thresholds.climatology import calculate_mhw
 from oisst import Catalogue
 
 MHW_BULK_CACHE = join(CACHDIR, "ohw", "thresholds", "bulk")
diff --git a/toolkit/cli/applications/mhw/thresholds/catalogue/__init__.py b/toolkit/cli/applications/mhw/thresholds/catalogue/__init__.py
new file mode 100644
index 00000000..af8db17d
--- /dev/null
+++ b/toolkit/cli/applications/mhw/thresholds/catalogue/__init__.py
@@ -0,0 +1,3 @@
+from cli.applications.mhw.thresholds.catalogue.update_cache import update_cache
+
+__all__ = ["update_cache"]
diff --git a/toolkit/cli/modules/mhw/thresholds/catalogue/update_cache.py b/toolkit/cli/applications/mhw/thresholds/catalogue/update_cache.py
similarity index 100%
rename from toolkit/cli/modules/mhw/thresholds/catalogue/update_cache.py
rename to toolkit/cli/applications/mhw/thresholds/catalogue/update_cache.py
diff --git a/toolkit/cli/applications/mhw/thresholds/climatology/__init__.py b/toolkit/cli/applications/mhw/thresholds/climatology/__init__.py
new file mode 100644
index 00000000..735f3264
--- /dev/null
+++ b/toolkit/cli/applications/mhw/thresholds/climatology/__init__.py
@@ -0,0 +1,4 @@
+from cli.applications.mhw.thresholds.climatology.daily import calculate_daily_clim
+from cli.applications.mhw.thresholds.climatology.define_mhw import calculate_mhw
+
+__all__ = ["calculate_daily_clim", "calculate_mhw"]
diff --git a/toolkit/cli/modules/mhw/thresholds/climatology/daily.py b/toolkit/cli/applications/mhw/thresholds/climatology/daily.py
similarity index 100%
rename from toolkit/cli/modules/mhw/thresholds/climatology/daily.py
rename to toolkit/cli/applications/mhw/thresholds/climatology/daily.py
diff --git a/toolkit/cli/modules/mhw/thresholds/climatology/define_mhw.py b/toolkit/cli/applications/mhw/thresholds/climatology/define_mhw.py
similarity index 100%
rename from toolkit/cli/modules/mhw/thresholds/climatology/define_mhw.py
rename to toolkit/cli/applications/mhw/thresholds/climatology/define_mhw.py
diff --git a/toolkit/cli/applications/ops/__init__.py b/toolkit/cli/applications/ops/__init__.py
new file mode 100644
index 00000000..13bb383b
--- /dev/null
+++ b/toolkit/cli/applications/ops/__init__.py
@@ -0,0 +1,5 @@
+from cli.applications.ops.download import download
+from cli.applications.ops.transform import transform
+from cli.applications.ops.load import load
+
+__all__ = ["download", "transform", "load"]
diff --git a/toolkit/cli/modules/ops/download/__init__.py b/toolkit/cli/applications/ops/download/__init__.py
similarity index 91%
rename from toolkit/cli/modules/ops/download/__init__.py
rename to toolkit/cli/applications/ops/download/__init__.py
index 9123e787..4c4a8765 100644
--- a/toolkit/cli/modules/ops/download/__init__.py
+++ b/toolkit/cli/applications/ops/download/__init__.py
@@ -1,8 +1,8 @@
 import os
 from datetime import datetime, timedelta
 from pathlib import Path
-from cli.modules.ops.download.mercator import download as mercator_download
-from cli.modules.ops.download.gfs import download as gfs_download
+from cli.applications.ops.download.mercator import download as mercator_download
+from cli.applications.ops.download.gfs import download as gfs_download
 
 
 def download(args):
diff --git a/toolkit/cli/modules/ops/download/gfs/__init__.py b/toolkit/cli/applications/ops/download/gfs/__init__.py
similarity index 98%
rename from toolkit/cli/modules/ops/download/gfs/__init__.py
rename to toolkit/cli/applications/ops/download/gfs/__init__.py
index 15eac392..e8dd0df9 100644
--- a/toolkit/cli/modules/ops/download/gfs/__init__.py
+++ b/toolkit/cli/applications/ops/download/gfs/__init__.py
@@ -1,6 +1,6 @@
 import asyncio
 from datetime import datetime, timedelta, time
-from cli.modules.ops.download.gfs.functions import (
+from cli.applications.ops.download.gfs.functions import (
     download_file,
     get_latest_available_dt,
     set_params,
diff --git a/toolkit/cli/modules/ops/download/gfs/functions.py b/toolkit/cli/applications/ops/download/gfs/functions.py
similarity index 100%
rename from toolkit/cli/modules/ops/download/gfs/functions.py
rename to toolkit/cli/applications/ops/download/gfs/functions.py
diff --git a/toolkit/cli/modules/ops/download/mercator/__init__.py b/toolkit/cli/applications/ops/download/mercator/__init__.py
similarity index 100%
rename from toolkit/cli/modules/ops/download/mercator/__init__.py
rename to toolkit/cli/applications/ops/download/mercator/__init__.py
diff --git a/toolkit/cli/modules/ops/load/__init__.py b/toolkit/cli/applications/ops/load/__init__.py
similarity index 94%
rename from toolkit/cli/modules/ops/load/__init__.py
rename to toolkit/cli/applications/ops/load/__init__.py
index 23647077..83a06d31 100644
--- a/toolkit/cli/modules/ops/load/__init__.py
+++ b/toolkit/cli/applications/ops/load/__init__.py
@@ -3,10 +3,11 @@
 from datetime import datetime
 from postgis import setup as installDb, drop as dropSchema, pool
 from config import PY_ENV
-from cli.modules.ops.load.raster2pgsql import register as refresh_rasters
-from cli.modules.ops.load.coordinates import upsert as refresh_coordinates
-from cli.modules.ops.load.values import upsert as refresh_values
-from cli.modules.ops.load.finalize import run as finalize
+from cli.applications.ops.load.raster2pgsql import register as refresh_rasters
+from cli.applications.ops.load.coordinates import upsert as refresh_coordinates
+from cli.applications.ops.load.values import upsert as refresh_values
+from cli.applications.ops.load.finalize import run as finalize
+
 
 def load(args):
     start_time = datetime.now()
diff --git a/toolkit/cli/modules/ops/load/coordinates/__init__.py b/toolkit/cli/applications/ops/load/coordinates/__init__.py
similarity index 100%
rename from toolkit/cli/modules/ops/load/coordinates/__init__.py
rename to toolkit/cli/applications/ops/load/coordinates/__init__.py
diff --git a/toolkit/cli/modules/ops/load/coordinates/coordinates.sql b/toolkit/cli/applications/ops/load/coordinates/coordinates.sql
similarity index 100%
rename from toolkit/cli/modules/ops/load/coordinates/coordinates.sql
rename to toolkit/cli/applications/ops/load/coordinates/coordinates.sql
diff --git a/toolkit/cli/modules/ops/load/finalize/__init__.py b/toolkit/cli/applications/ops/load/finalize/__init__.py
similarity index 100%
rename from toolkit/cli/modules/ops/load/finalize/__init__.py
rename to toolkit/cli/applications/ops/load/finalize/__init__.py
diff --git a/toolkit/cli/modules/ops/load/models.yml b/toolkit/cli/applications/ops/load/models.yml
similarity index 100%
rename from toolkit/cli/modules/ops/load/models.yml
rename to toolkit/cli/applications/ops/load/models.yml
diff --git a/toolkit/cli/modules/ops/load/raster2pgsql/__init__.py b/toolkit/cli/applications/ops/load/raster2pgsql/__init__.py
similarity index 100%
rename from toolkit/cli/modules/ops/load/raster2pgsql/__init__.py
rename to toolkit/cli/applications/ops/load/raster2pgsql/__init__.py
diff --git a/toolkit/cli/modules/ops/load/raster2pgsql/update-raster_xref_run.sql b/toolkit/cli/applications/ops/load/raster2pgsql/update-raster_xref_run.sql
similarity index 100%
rename from toolkit/cli/modules/ops/load/raster2pgsql/update-raster_xref_run.sql
rename to toolkit/cli/applications/ops/load/raster2pgsql/update-raster_xref_run.sql
diff --git a/toolkit/cli/modules/ops/load/values/__init__.py b/toolkit/cli/applications/ops/load/values/__init__.py
similarity index 83%
rename from toolkit/cli/modules/ops/load/values/__init__.py
rename to toolkit/cli/applications/ops/load/values/__init__.py
index 491c162d..6b16e5a2 100644
--- a/toolkit/cli/modules/ops/load/values/__init__.py
+++ b/toolkit/cli/applications/ops/load/values/__init__.py
@@ -1,4 +1,4 @@
-from cli.modules.ops.load.values.load_band import load
+from cli.applications.ops.load.values.load_band import load
 
 
 def upsert(runid, start_time, depths, datetimes, total_depth_levels):
diff --git a/toolkit/cli/modules/ops/load/values/load_band.py b/toolkit/cli/applications/ops/load/values/load_band.py
similarity index 100%
rename from toolkit/cli/modules/ops/load/values/load_band.py
rename to toolkit/cli/applications/ops/load/values/load_band.py
diff --git a/toolkit/cli/modules/ops/transform/__init__.py b/toolkit/cli/applications/ops/transform/__init__.py
similarity index 98%
rename from toolkit/cli/modules/ops/transform/__init__.py
rename to toolkit/cli/applications/ops/transform/__init__.py
index 598b8c2a..13cf5a49 100644
--- a/toolkit/cli/modules/ops/transform/__init__.py
+++ b/toolkit/cli/applications/ops/transform/__init__.py
@@ -2,8 +2,8 @@
 import numpy as np
 import os
 from datetime import timedelta, datetime
-from cli.modules.ops.transform.depth_functions import z_levels
-from cli.modules.ops.transform.functions import hour_rounder, u2rho_4d, v2rho_4d
+from cli.applications.ops.transform.depth_functions import z_levels
+from cli.applications.ops.transform.functions import hour_rounder, u2rho_4d, v2rho_4d
 import subprocess
 
 # All dates in the CROCO output are represented
diff --git a/toolkit/cli/modules/ops/transform/depth_functions.py b/toolkit/cli/applications/ops/transform/depth_functions.py
similarity index 100%
rename from toolkit/cli/modules/ops/transform/depth_functions.py
rename to toolkit/cli/applications/ops/transform/depth_functions.py
diff --git a/toolkit/cli/modules/ops/transform/functions.py b/toolkit/cli/applications/ops/transform/functions.py
similarity index 100%
rename from toolkit/cli/modules/ops/transform/functions.py
rename to toolkit/cli/applications/ops/transform/functions.py
diff --git a/toolkit/cli/modules/update/__init__.py b/toolkit/cli/applications/update/__init__.py
similarity index 100%
rename from toolkit/cli/modules/update/__init__.py
rename to toolkit/cli/applications/update/__init__.py
diff --git a/toolkit/cli/modules/update/update_bashrc.py b/toolkit/cli/applications/update/update_bashrc.py
similarity index 100%
rename from toolkit/cli/modules/update/update_bashrc.py
rename to toolkit/cli/applications/update/update_bashrc.py
diff --git a/toolkit/cli/commands/__init__.py b/toolkit/cli/commands/__init__.py
deleted file mode 100644
index 29fc1cee..00000000
--- a/toolkit/cli/commands/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from cli.commands import lacce, mhw, ops, kerchunk, update
-
-__all__ = ["lacce", "mhw", "ops", "kerchunk", "update"]
diff --git a/toolkit/cli/define/__init__.py b/toolkit/cli/define/__init__.py
new file mode 100644
index 00000000..45902bf7
--- /dev/null
+++ b/toolkit/cli/define/__init__.py
@@ -0,0 +1,3 @@
+from cli.define import lacce, mhw, ops, kerchunk, update
+
+__all__ = ["lacce", "mhw", "ops", "kerchunk", "update"]
diff --git a/toolkit/cli/commands/kerchunk/__init__.py b/toolkit/cli/define/kerchunk/__init__.py
similarity index 100%
rename from toolkit/cli/commands/kerchunk/__init__.py
rename to toolkit/cli/define/kerchunk/__init__.py
diff --git a/toolkit/cli/commands/lacce/__init__.py b/toolkit/cli/define/lacce/__init__.py
similarity index 100%
rename from toolkit/cli/commands/lacce/__init__.py
rename to toolkit/cli/define/lacce/__init__.py
diff --git a/toolkit/cli/commands/mhw/__init__.py b/toolkit/cli/define/mhw/__init__.py
similarity index 100%
rename from toolkit/cli/commands/mhw/__init__.py
rename to toolkit/cli/define/mhw/__init__.py
diff --git a/toolkit/cli/commands/ops/__init__.py b/toolkit/cli/define/ops/__init__.py
similarity index 100%
rename from toolkit/cli/commands/ops/__init__.py
rename to toolkit/cli/define/ops/__init__.py
diff --git a/toolkit/cli/commands/update/__init__.py b/toolkit/cli/define/update/__init__.py
similarity index 100%
rename from toolkit/cli/commands/update/__init__.py
rename to toolkit/cli/define/update/__init__.py
diff --git a/toolkit/cli/exe/kerchunk/__init__.py b/toolkit/cli/exe/kerchunk/__init__.py
deleted file mode 100644
index 858423fe..00000000
--- a/toolkit/cli/exe/kerchunk/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from cli.modules.kerchunk import run as run_kerchunker
-
-def run(cmd, args):
-    if args.kerchunk_command == "run":
-        run_kerchunker(args)
-    else:
-        print(cmd.format_help())
\ No newline at end of file
diff --git a/toolkit/cli/exe/mhw/__init__.py b/toolkit/cli/exe/mhw/__init__.py
deleted file mode 100644
index cb5059b0..00000000
--- a/toolkit/cli/exe/mhw/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from cli.modules.mhw import start
-
-def run(cmd, args):
-    if args.mhw_command == "start":
-        start(args)
-    else:
-        print(cmd.format_help())
\ No newline at end of file
diff --git a/toolkit/cli/modules/__init__.py b/toolkit/cli/modules/__init__.py
deleted file mode 100644
index 50f2fad7..00000000
--- a/toolkit/cli/modules/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from cli.modules import lacce, mhw, ops, kerchunk, update
-
-__all__ = ["lacce", "mhw", "ops", "kerchunk", "update"]
diff --git a/toolkit/cli/modules/kerchunk/__init__.py b/toolkit/cli/modules/kerchunk/__init__.py
deleted file mode 100644
index af24bc3d..00000000
--- a/toolkit/cli/modules/kerchunk/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from cli.modules.kerchunk.run import run
-
-__all__ = ['run']
\ No newline at end of file
diff --git a/toolkit/cli/modules/mhw/__init__.py b/toolkit/cli/modules/mhw/__init__.py
deleted file mode 100644
index 55d6640b..00000000
--- a/toolkit/cli/modules/mhw/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from cli.modules.mhw.start import start
-from cli.modules.mhw.thresholds import create_thresholds
-
-__all__ = ['start', 'create_thresholds']
\ No newline at end of file
diff --git a/toolkit/cli/modules/mhw/thresholds/catalogue/__init__.py b/toolkit/cli/modules/mhw/thresholds/catalogue/__init__.py
deleted file mode 100644
index eb6ab4c6..00000000
--- a/toolkit/cli/modules/mhw/thresholds/catalogue/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from cli.modules.mhw.thresholds.catalogue.update_cache import update_cache
-
-__all__ = ['update_cache']
\ No newline at end of file
diff --git a/toolkit/cli/modules/mhw/thresholds/climatology/__init__.py b/toolkit/cli/modules/mhw/thresholds/climatology/__init__.py
deleted file mode 100644
index f1fa3b0e..00000000
--- a/toolkit/cli/modules/mhw/thresholds/climatology/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from cli.modules.mhw.thresholds.climatology.daily import calculate_daily_clim
-from cli.modules.mhw.thresholds.climatology.define_mhw import calculate_mhw
-
-__all__ = ['calculate_daily_clim','calculate_mhw']
\ No newline at end of file
diff --git a/toolkit/cli/modules/ops/__init__.py b/toolkit/cli/modules/ops/__init__.py
deleted file mode 100644
index 1361bb6b..00000000
--- a/toolkit/cli/modules/ops/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from cli.modules.ops.download import download
-from cli.modules.ops.transform import transform
-from cli.modules.ops.load import load
-
-__all__ = ["download", "transform", "load"]
diff --git a/toolkit/cli/exe/__init__.py b/toolkit/cli/parse/__init__.py
similarity index 50%
rename from toolkit/cli/exe/__init__.py
rename to toolkit/cli/parse/__init__.py
index 5328588b..f1e7c22d 100644
--- a/toolkit/cli/exe/__init__.py
+++ b/toolkit/cli/parse/__init__.py
@@ -1,3 +1,3 @@
-from cli.exe import lacce, mhw, ops, kerchunk, update
+from cli.parse import lacce, mhw, ops, kerchunk, update
 
 __all__ = ["lacce", "mhw", "ops", "kerchunk", "update"]
diff --git a/toolkit/cli/parse/kerchunk/__init__.py b/toolkit/cli/parse/kerchunk/__init__.py
new file mode 100644
index 00000000..1d3234ad
--- /dev/null
+++ b/toolkit/cli/parse/kerchunk/__init__.py
@@ -0,0 +1,5 @@
+def parse(cmd, args, module):
+    if args.kerchunk_command == "run":
+        return module.run
+    else:
+        print(cmd.format_help())
diff --git a/toolkit/cli/exe/lacce/__init__.py b/toolkit/cli/parse/lacce/__init__.py
similarity index 64%
rename from toolkit/cli/exe/lacce/__init__.py
rename to toolkit/cli/parse/lacce/__init__.py
index 79983218..739257fd 100644
--- a/toolkit/cli/exe/lacce/__init__.py
+++ b/toolkit/cli/parse/lacce/__init__.py
@@ -1,7 +1,7 @@
-def run(cmd, args):
+def parse(cmd, args, module):
     input = args.input
     output = args.output
     if input and output:
         print("LACCE", input, output)
-        return
+        return lambda: print("Not implemented")
     print(cmd.format_help())
diff --git a/toolkit/cli/parse/mhw/__init__.py b/toolkit/cli/parse/mhw/__init__.py
new file mode 100644
index 00000000..6526e97a
--- /dev/null
+++ b/toolkit/cli/parse/mhw/__init__.py
@@ -0,0 +1,5 @@
+def parse(cmd, args, module):
+    if args.mhw_command == "start":
+        return module.start
+    else:
+        print(cmd.format_help())
diff --git a/toolkit/cli/exe/ops/__init__.py b/toolkit/cli/parse/ops/__init__.py
similarity index 53%
rename from toolkit/cli/exe/ops/__init__.py
rename to toolkit/cli/parse/ops/__init__.py
index 188b3a54..0d3e854f 100644
--- a/toolkit/cli/exe/ops/__init__.py
+++ b/toolkit/cli/parse/ops/__init__.py
@@ -1,12 +1,9 @@
-from cli.modules.ops import download, load, transform
-
-
-def run(cmd, args):
+def parse(cmd, args, module):
     if args.ops_command == "download":
-        download(args)
+        return module.download
     elif args.ops_command == "transform":
-        transform(args)
+        return module.transform
     elif args.ops_command == "load":
-        load(args)
+        return module.load
     else:
         print(cmd.format_help())
diff --git a/toolkit/cli/exe/update/__init__.py b/toolkit/cli/parse/update/__init__.py
similarity index 61%
rename from toolkit/cli/exe/update/__init__.py
rename to toolkit/cli/parse/update/__init__.py
index 6384f102..553f1b16 100644
--- a/toolkit/cli/exe/update/__init__.py
+++ b/toolkit/cli/parse/update/__init__.py
@@ -1,13 +1,8 @@
-from cli.modules.update.update_bashrc import update_bashrc
-
-
-def run(cmd, args):
+def run(cmd, args, module):
     version = args.version
     reset = args.reset
     if reset and version:
         raise Exception("Please specify either reset or version flags")
-
     if version or reset:
-        update_bashrc(args)
-        return
+        return module.update_bashrc
     print(cmd.format_help())