From 278076e8e926612a5c63c07fd4d12739ee4bdc11 Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Wed, 9 Oct 2024 18:04:45 +0200
Subject: [PATCH 1/7] revisit CLI: run and l2b

---
 aprofiles/cli/__init__.py                     |   2 +-
 aprofiles/cli/{aprocess.py => apro.py}        |  40 ++++--
 aprofiles/cli/utils/__init__.py               |   2 +-
 .../utils/{json_calendar.py => calendar.py}   |   0
 .../{json_climatology.py => climatology.py}   |   0
 aprofiles/cli/utils/l2b.py                    |  38 +++++
 aprofiles/cli/utils/{json_map.py => map.py}   |   0
 docs/changelog.md                             |   7 +
 docs/cli.md                                   | 134 ++++++++++++------
 pyproject.toml                                |   5 +-
 10 files changed, 169 insertions(+), 59 deletions(-)
 rename aprofiles/cli/{aprocess.py => apro.py} (82%)
 rename aprofiles/cli/utils/{json_calendar.py => calendar.py} (100%)
 rename aprofiles/cli/utils/{json_climatology.py => climatology.py} (100%)
 create mode 100644 aprofiles/cli/utils/l2b.py
 rename aprofiles/cli/utils/{json_map.py => map.py} (100%)

diff --git a/aprofiles/cli/__init__.py b/aprofiles/cli/__init__.py
index c8c942f..f5cc7c6 100644
--- a/aprofiles/cli/__init__.py
+++ b/aprofiles/cli/__init__.py
@@ -1 +1 @@
-from .utils import config, json_calendar, json_climatology, json_map, workflow
\ No newline at end of file
+from .utils import config, calendar, climatology, map, l2b, workflow
\ No newline at end of file
diff --git a/aprofiles/cli/aprocess.py b/aprofiles/cli/apro.py
similarity index 82%
rename from aprofiles/cli/aprocess.py
rename to aprofiles/cli/apro.py
index c79d779..86ddbd3 100755
--- a/aprofiles/cli/aprocess.py
+++ b/aprofiles/cli/apro.py
@@ -22,7 +22,7 @@ class InstrumentType(str, Enum):
     cl61 = "CL61"
 
 @app.command()
-def main(
+def run(
     _dates: List[datetime] = typer.Option(
         [], "--date", formats=["%Y-%m-%d"], help="📅 Processing date."
     ),
@@ -66,9 +66,9 @@ def main(
     progress_bar: bool = typer.Option(True, help="⌛ Show progress bar."),
 ):
     """
-    Run aprofiles standard workflow for given dates, optionally for specific instruments types.
+    run aprofiles standard workflow for given dates and specific instruments types
     
-    See some examples here: https://a-profiles.readthedocs.io/en/latest/cli.html
+    see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)
     """
 
     #typer.echo(f"dates: {dates}, today: {today}, yesterday: {yesterday}, from: {_from}, to: {_to}, instruments_types: {instruments_types}, multiprocessing: {multiprocessing}")
@@ -142,13 +142,13 @@ def main(
             calname = f"{yyyy}-{mm}-cal.json"
             path = Path(basedir_out, yyyy, mm, calname)
             if not path.is_file():
-                utils.json_calendar.make_calendar(basedir_out, yyyy, mm, calname)
+                utils.calendar.make_calendar(basedir_out, yyyy, mm, calname)
 
             # list all files in out directory
             onlyfiles = [str(e) for e in datepath.iterdir() if e.is_file()]
             # add to calendar
             for file in track(onlyfiles, description="calendar     ", disable=disable_progress_bar):
-                utils.json_calendar.add_to_calendar(file, basedir_out, yyyy, mm, dd, calname)
+                utils.calendar.add_to_calendar(file, basedir_out, yyyy, mm, dd, calname)
             
         
         if update_map:
@@ -156,13 +156,13 @@ def main(
             mapname = f"{yyyy}-{mm}-map.json"
             path = Path(basedir_out, yyyy, mm, mapname)
             if not path.is_file():
-                utils.json_map.make_map(basedir_out, yyyy, mm, mapname)
+                utils.map.make_map(basedir_out, yyyy, mm, mapname)
 
             # list all files in out directory
             onlyfiles = [str(e) for e in datepath.iterdir() if e.is_file()]
             # add to map
             for file in track(onlyfiles, description="map          ", disable=disable_progress_bar):
-                utils.json_map.add_to_map(file, basedir_out, yyyy, mm, dd, mapname)
+                utils.map.add_to_map(file, basedir_out, yyyy, mm, dd, mapname)
 
     if update_climatology:
         # list all files in out directory
@@ -177,7 +177,7 @@ def main(
                 task = progress.add_task(total=len(stations_id), description=f"clim.      :rocket:", visible=not disable_progress_bar)
                 with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:
                     futures = [executor.submit(
-                        utils.json_climatology.compute_climatology,
+                        utils.climatology.compute_climatology,
                         basedir_out, 
                         station_id, 
                         season_variables=["extinction"],
@@ -189,8 +189,30 @@ def main(
                         progress.update(task, advance=1)
         else:
             for station_id in track(stations_id, description='clim.        ', disable=disable_progress_bar):
-                utils.json_climatology.compute_climatology(basedir_out, station_id, season_variables=["extinction"], all_variables=["aod", "lidar_ratio"], aerosols_only=True)
+                utils.climatology.compute_climatology(basedir_out, station_id, season_variables=["extinction"], all_variables=["aod", "lidar_ratio"], aerosols_only=True)
 
 
+@app.command()
+def l2b(
+        basedir_in: Path = typer.Option(
+            "data/v-profiles", exists=True, readable=True, help="📂 Base path for input data."
+        ),
+        basedir_out: Path = typer.Option(
+            "data/l2b", exists=True, writable=True, help="📂 Base path for output data."
+        ),
+        progress_bar: bool = typer.Option(True, help="⌛ Show progress bar.")
+    ):
+    """
+    make E-PROFILE L2b files out of AP files
+    """
+
+    # if basedir_in is "data/v-profiles", use today's date to find the directory
+    if basedir_in == Path("data/v-profiles"):
+        # get todays date
+        today = datetime.today()
+        basedir_in = Path(basedir_in, today.strftime('%Y'), today.strftime('%m'), today.strftime('%d'))
+    
+    utils.l2b.make_files(basedir_in, basedir_out, progress_bar)
+
 if __name__ == "__main__":
     app()
diff --git a/aprofiles/cli/utils/__init__.py b/aprofiles/cli/utils/__init__.py
index 95f7cbf..089bb83 100644
--- a/aprofiles/cli/utils/__init__.py
+++ b/aprofiles/cli/utils/__init__.py
@@ -1 +1 @@
-from . import json_calendar, json_climatology, json_map, config, workflow
\ No newline at end of file
+from . import calendar, climatology, map, l2b, config, workflow
\ No newline at end of file
diff --git a/aprofiles/cli/utils/json_calendar.py b/aprofiles/cli/utils/calendar.py
similarity index 100%
rename from aprofiles/cli/utils/json_calendar.py
rename to aprofiles/cli/utils/calendar.py
diff --git a/aprofiles/cli/utils/json_climatology.py b/aprofiles/cli/utils/climatology.py
similarity index 100%
rename from aprofiles/cli/utils/json_climatology.py
rename to aprofiles/cli/utils/climatology.py
diff --git a/aprofiles/cli/utils/l2b.py b/aprofiles/cli/utils/l2b.py
new file mode 100644
index 0000000..97ccd1a
--- /dev/null
+++ b/aprofiles/cli/utils/l2b.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+import os
+import sys
+from pathlib import Path
+
+from glob import glob
+
+import xarray as xr
+import pandas as pd
+from rich.progress import track
+
+def make_files(path_in: Path, path_out: Path, progress_bar: bool) -> None:
+    
+    # list all AP files in path_in
+    files = glob(f"{path_in}/AP*nc")
+
+    for f in track(files, description=f"Reading AP files", disable=not progress_bar):
+
+        ds = xr.open_dataset(f, decode_times=True, chunks=-1).load()
+        # get unique id and extract yyyymmdd from first time step
+        unique_id = f"{ds.attrs['wigos_station_id']}_{ds.attrs['instrument_id']}"
+        yyyymmdd = str(ds.time.data[0].astype('M8[D]')).replace('-','')        
+        
+        ntimes = ds.time.size
+        if ntimes < 60:
+            myrange = range(ntimes)
+        else:
+            myrange = range(ntimes-12, ntimes)
+
+        for i in myrange:
+            ds1t = ds.isel(time=i)
+            mmhh = pd.to_datetime(ds1t.time.data).strftime('%H%M')
+            file_name = Path(path_out, f"{unique_id}_{yyyymmdd}{mmhh}.nc")
+            ds1t.to_netcdf('out.nc')
+            os.rename('out.nc',file_name)
+
+
diff --git a/aprofiles/cli/utils/json_map.py b/aprofiles/cli/utils/map.py
similarity index 100%
rename from aprofiles/cli/utils/json_map.py
rename to aprofiles/cli/utils/map.py
diff --git a/docs/changelog.md b/docs/changelog.md
index 2ee0c72..0146cf2 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,13 @@
 
 :material-history:{ style="text-align: center; font-size: xx-large; display: block" }
 
+## 0.10.0
+Oct 10, 2024
+
+- revisit CLI: two commands
+    - `apro run` (formerly `aprocess`: run standard workflow)
+    - `apro l2b` (creates L2b files out of AP files)
+
 ## 0.9.7
 Oct 3, 2024
 
diff --git a/docs/cli.md b/docs/cli.md
index 1e655b5..343f27b 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -4,7 +4,7 @@
 
 For facilitating the processing of the measurements in routine, a
 Command Line Interface (CLI) has been developed:
-[cli/aprocess.py](cli/aprocess.py){: .download}
+[cli/apro.py](cli/apro.py){: .download}
 
 In the current version, the CLI has 3 possible actions:
 
@@ -31,83 +31,125 @@ poetry install --extras cli
 
 ## Documentation
 
-    aprocess --help
-
-returns the documentation of the CLI, with all available options.
+`apro` commands which can be listed with
 
+``` console
+apro --help
+                                                                                                                                       
+ Usage: apro [OPTIONS] COMMAND [ARGS]...                                                                                               
+                                                                                                                                       
+╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --install-completion          Install completion for the current shell.                                                             │
+│ --show-completion             Show completion for the current shell, to copy it or customize the installation.                      │
+│ --help                        Show this message and exit.                                                                           │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ l2b   make E-PROFILE L2b files out of AP files                                                                                      │
+│ run   run aprofiles standard workflow for given dates and specific instruments types                                                │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
-$ aprocess --help
-
 
-Usage: aprocess [OPTIONS]                                                                                                                                    
 
-Run aprofiles standard workflow for given dates, optionally for specific instruments types.                                                                  
-See some examples here: https://a-profiles.readthedocs.io/en/latest/cli.html                                                                                 
+### `run` command
 
-╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --date                                             [%Y-%m-%d]              📅 Processing date.                                                                     │
-│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                                                        │
-│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]                                               │
-│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]                                            │
-│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]                                    │
-│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed. [default: CHM15k, Mini-MPL]            │
-│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode. [default: no-multiprocessing]                              │
-│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode is enabled). [env var: NSLOTS]    │
-│                                                                            [default: 2]                                                                            │
-│ --basedir-in                                       PATH                    📂 Base path for input data. [default: data/e-profile]                                  │
-│ --basedir-out                                      PATH                    📂 Base path for output data. [default: data/v-profiles]                                │
-│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file. [default: config]                                │
-│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                                                  │
-│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]                                           │
-│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                                                     │
-│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]                                     │
-│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]                                           │
-│ --install-completion                                                       Install completion for the current shell.                                               │
-│ --show-completion                                                          Show completion for the current shell, to copy it or customize the installation.        │
-│ --help                                                                     Show this message and exit.                                                             │
-╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+```
+apro run --help
+                                                                                                                                       
+ Usage: apro run [OPTIONS]                                                                                                             
+                                                                                                                                       
+ run aprofiles standard workflow for given dates and specific instruments types                                                        
+ see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)                                                           
+                                                                                                                                       
+╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --date                                             [%Y-%m-%d]              📅 Processing date.                                      │
+│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                         │
+│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]                │
+│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]             │
+│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]     │
+│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed.         │
+│                                                                            [default: CHM15k, Mini-MPL]                              │
+│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode.                             │
+│                                                                            [default: no-multiprocessing]                            │
+│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode i… │
+│                                                                            enabled).                                                │
+│                                                                            [env var: NSLOTS]                                        │
+│                                                                            [default: 2]                                             │
+│ --basedir-in                                       PATH                    📂 Base path for input data. [default: data/e-profile]   │
+│ --basedir-out                                      PATH                    📂 Base path for output data. [default: data/v-profiles] │
+│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file. [default: config] │
+│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                   │
+│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]            │
+│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                      │
+│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]      │
+│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]            │
+│ --help                                                                     Show this message and exit.                              │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
-## Basic uses
+#### Examples
 
-### run a specific date
+##### run a specific date
 
 ```
-aprocess --date 2021-09-09
+apro run --date 2021-09-09
 ```
 
-### run today\'s files
+##### run today\'s files
 
 ```
-aprocess --today
+apro run --today
 ```
 
-### run yesterday\'s files
+##### run yesterday\'s files
 
 ```
-aprocess --yesterday
+apro run --yesterday
 ```
 
-## More advanced uses
-
 It is possible to combine different options.
 
-### run today\'s and yesterday\'s files for CHM15k only
+##### run today\'s and yesterday\'s files for CHM15k only
 
 ```
-aprocess --today --yesterday --instruments-type CHM15k
+apro run --today --yesterday --instruments-type CHM15k
 ```
 
-### update only calendar files for 2021
+##### update only calendar files for 2021
 
 ```
-aprocess --from 2021-01-01 --to 2021-12-31 --no-update-data --no-update-map
+apro run --from 2021-01-01 --to 2021-12-31 --no-update-data --no-update-map
 ```
 
-### use multiprocessing
+##### use multiprocessing
 
 The data processing can be run in parallel by using the
 [`multiprocessing`] option :
 ```
-aprocess --today --yesterday --multiprocessing
+apro run --today --yesterday --multiprocessing
+```
+
+
+### `l2b` command
+
+```
+apro l2b --help
+                                                                                                                                       
+ Usage: apro l2b [OPTIONS]                                                                                                             
+                                                                                                                                       
+ make E-PROFILE L2b files out of AP files                                                                                              
+                                                                                                                                       
+╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --basedir-in                           PATH  📂 Base path for input data. [default: data/v-profiles]                                │
+│ --basedir-out                          PATH  📂 Base path for output data. [default: data/l2b]                                      │
+│ --progress-bar    --no-progress-bar          ⌛ Show progress bar. [default: progress-bar]                                          │
+│ --help                                       Show this message and exit.                                                            │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
+
+#### Examples
+
+##### make L2b files out of today's AP files in default directory
+
+```bash
+apro l2b 
+```
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index a1fff5f..41dbfd2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,12 @@
 [tool.poetry]
 name = "aprofiles"
-version = "0.9.7"
+version = "0.10.0"
 description = "Analysis of atmospheric profilers measurements"
 authors = ["augustinm <augustinm@met.no>"]
 license = "GPL-3.0"
 
 [tool.poetry.scripts]
-aprocess = {callable = "aprofiles.cli.aprocess:app", extras = ["cli"]}
+apro = {callable = "aprofiles.cli.apro:app", extras = ["cli"]}
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.13"
@@ -39,6 +39,7 @@ pymdown-extensions = "^10.10"
 mkdocstrings = {extras = ["python"], version = "^0.26.1"}
 markdown-include = "^0.8.1"
 mkdocs-copy = "^0.0.1"
+ipywidgets = "^8.1.5"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

From 119b2609c3afddcfa8d5677797ac2e1c8c665d68 Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Wed, 9 Oct 2024 18:12:51 +0200
Subject: [PATCH 2/7] replace basedir by path

---
 aprofiles/cli/apro.py              | 40 +++++++++++++++---------------
 aprofiles/cli/utils/calendar.py    | 10 ++++----
 aprofiles/cli/utils/climatology.py |  6 ++---
 aprofiles/cli/utils/map.py         | 10 ++++----
 4 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/aprofiles/cli/apro.py b/aprofiles/cli/apro.py
index 86ddbd3..35800f8 100755
--- a/aprofiles/cli/apro.py
+++ b/aprofiles/cli/apro.py
@@ -45,10 +45,10 @@ def run(
     workers: int = typer.Option(
         2, "--workers", min=1, envvar="NSLOTS", help="👷 Number of workers (NSLOTS, if multiprocessing mode is enabled)."
     ),
-    basedir_in: Path = typer.Option(
+    path_in: Path = typer.Option(
         "data/e-profile", exists=True, readable=True, help="📂 Base path for input data."
     ),
-    basedir_out: Path = typer.Option(
+    path_out: Path = typer.Option(
         "data/v-profiles",
         exists=True,
         writable=True,
@@ -110,7 +110,7 @@ def run(
         dd = str(date.day).zfill(2)
 
         # list all files in in directory
-        datepath = Path(basedir_in, yyyy, mm, dd)
+        datepath = Path(path_in, yyyy, mm, dd)
         onlyfiles = [str(e) for e in datepath.iterdir() if e.is_file()]
 
         # data processing
@@ -123,7 +123,7 @@ def run(
                             utils.workflow.workflow, 
                             path=file, 
                             instruments_types=instruments_types, 
-                            base_dir=basedir_out, CFG=CFG, verbose=False
+                            base_dir=path_out, CFG=CFG, verbose=False
                         )
                         for file in onlyfiles]
                         for future in concurrent.futures.as_completed(futures):
@@ -131,38 +131,38 @@ def run(
             else:
                 for file in track(onlyfiles, description=f"{date.strftime('%Y-%m-%d')}   ", disable=disable_progress_bar):
                     utils.workflow.workflow(
-                        file, instruments_types, basedir_out, CFG, verbose=False
+                        file, instruments_types, path_out, CFG, verbose=False
                     )
         
         # list all files in out directory
-        datepath = Path(basedir_out, yyyy, mm, dd)
+        datepath = Path(path_out, yyyy, mm, dd)
 
         if update_calendar:
             # create calendar
             calname = f"{yyyy}-{mm}-cal.json"
-            path = Path(basedir_out, yyyy, mm, calname)
+            path = Path(path_out, yyyy, mm, calname)
             if not path.is_file():
-                utils.calendar.make_calendar(basedir_out, yyyy, mm, calname)
+                utils.calendar.make_calendar(path_out, yyyy, mm, calname)
 
             # list all files in out directory
             onlyfiles = [str(e) for e in datepath.iterdir() if e.is_file()]
             # add to calendar
             for file in track(onlyfiles, description="calendar     ", disable=disable_progress_bar):
-                utils.calendar.add_to_calendar(file, basedir_out, yyyy, mm, dd, calname)
+                utils.calendar.add_to_calendar(file, path_out, yyyy, mm, dd, calname)
             
         
         if update_map:
             # create map
             mapname = f"{yyyy}-{mm}-map.json"
-            path = Path(basedir_out, yyyy, mm, mapname)
+            path = Path(path_out, yyyy, mm, mapname)
             if not path.is_file():
-                utils.map.make_map(basedir_out, yyyy, mm, mapname)
+                utils.map.make_map(path_out, yyyy, mm, mapname)
 
             # list all files in out directory
             onlyfiles = [str(e) for e in datepath.iterdir() if e.is_file()]
             # add to map
             for file in track(onlyfiles, description="map          ", disable=disable_progress_bar):
-                utils.map.add_to_map(file, basedir_out, yyyy, mm, dd, mapname)
+                utils.map.add_to_map(file, path_out, yyyy, mm, dd, mapname)
 
     if update_climatology:
         # list all files in out directory
@@ -178,7 +178,7 @@ def run(
                 with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:
                     futures = [executor.submit(
                         utils.climatology.compute_climatology,
-                        basedir_out, 
+                        path_out, 
                         station_id, 
                         season_variables=["extinction"],
                         all_variables=["aod", "lidar_ratio"],
@@ -189,15 +189,15 @@ def run(
                         progress.update(task, advance=1)
         else:
             for station_id in track(stations_id, description='clim.        ', disable=disable_progress_bar):
-                utils.climatology.compute_climatology(basedir_out, station_id, season_variables=["extinction"], all_variables=["aod", "lidar_ratio"], aerosols_only=True)
+                utils.climatology.compute_climatology(path_out, station_id, season_variables=["extinction"], all_variables=["aod", "lidar_ratio"], aerosols_only=True)
 
 
 @app.command()
 def l2b(
-        basedir_in: Path = typer.Option(
+        path_in: Path = typer.Option(
             "data/v-profiles", exists=True, readable=True, help="📂 Base path for input data."
         ),
-        basedir_out: Path = typer.Option(
+        path_out: Path = typer.Option(
             "data/l2b", exists=True, writable=True, help="📂 Base path for output data."
         ),
         progress_bar: bool = typer.Option(True, help="⌛ Show progress bar.")
@@ -206,13 +206,13 @@ def l2b(
     make E-PROFILE L2b files out of AP files
     """
 
-    # if basedir_in is "data/v-profiles", use today's date to find the directory
-    if basedir_in == Path("data/v-profiles"):
+    # if path_in is "data/v-profiles", use today's date to find the directory
+    if path_in == Path("data/v-profiles"):
         # get todays date
         today = datetime.today()
-        basedir_in = Path(basedir_in, today.strftime('%Y'), today.strftime('%m'), today.strftime('%d'))
+        path_in = Path(path_in, today.strftime('%Y'), today.strftime('%m'), today.strftime('%d'))
     
-    utils.l2b.make_files(basedir_in, basedir_out, progress_bar)
+    utils.l2b.make_files(path_in, path_out, progress_bar)
 
 if __name__ == "__main__":
     app()
diff --git a/aprofiles/cli/utils/calendar.py b/aprofiles/cli/utils/calendar.py
index 91dbc0c..e3fc298 100644
--- a/aprofiles/cli/utils/calendar.py
+++ b/aprofiles/cli/utils/calendar.py
@@ -7,12 +7,12 @@
 import xarray as xr
 
 
-def make_calendar(base_dir, yyyy, mm, calname):
+def make_calendar(path, yyyy, mm, calname):
     # one calendar, per month
-    with open(Path(base_dir, yyyy, mm, calname), 'w') as json_file:
+    with open(Path(path, yyyy, mm, calname), 'w') as json_file:
         json.dump({}, json_file)
 
-def add_to_calendar(fn, base_dir, yyyy, mm, dd, calname):
+def add_to_calendar(fn, path, yyyy, mm, dd, calname):
     # calendar collects the number of inversions with no low-level clouds (<6km) at each station
     # for each station, write number of each scene class (aer, cloud<6km, cloud>6km, )
     
@@ -28,7 +28,7 @@ def add_to_calendar(fn, base_dir, yyyy, mm, dd, calname):
     scene_counts['total'] = len(ds.retrieval_scene.data)
 
     # open current calendar
-    with open(Path(base_dir, yyyy, mm, calname), 'r') as json_file:
+    with open(Path(path, yyyy, mm, calname), 'r') as json_file:
         data = json.load(json_file)
     json_file.close()        
 
@@ -39,5 +39,5 @@ def add_to_calendar(fn, base_dir, yyyy, mm, dd, calname):
     data[station_id][dd] = scene_counts
 
     # write new calendar
-    with open(Path(base_dir, yyyy, mm, calname), 'w') as json_file:
+    with open(Path(path, yyyy, mm, calname), 'w') as json_file:
         json.dump(data, json_file)
diff --git a/aprofiles/cli/utils/climatology.py b/aprofiles/cli/utils/climatology.py
index fc261b6..b8713d4 100644
--- a/aprofiles/cli/utils/climatology.py
+++ b/aprofiles/cli/utils/climatology.py
@@ -10,10 +10,10 @@
 import xarray as xr
 
 
-def compute_climatology(basedir, station_id, season_variables, all_variables, aerosols_only):
+def compute_climatology(path, station_id, season_variables, all_variables, aerosols_only):
     # get all files
     station_files = []
-    for root, dirs, files in os.walk(basedir, followlinks=True):
+    for root, dirs, files in os.walk(path, followlinks=True):
         for file in files:
             if station_id in file and file.endswith(".nc"):
                 station_files.append(os.path.join(root, file))
@@ -67,7 +67,7 @@ def compute_climatology(basedir, station_id, season_variables, all_variables, ae
         multivars_dict["attrs"] = attrs
 
         # define path
-        clim_path = Path(basedir, "climato")
+        clim_path = Path(path, "climato")
         # create directory if does not exist
         clim_path.mkdir(parents=True, exist_ok=True)
 
diff --git a/aprofiles/cli/utils/map.py b/aprofiles/cli/utils/map.py
index d251a23..25f8036 100644
--- a/aprofiles/cli/utils/map.py
+++ b/aprofiles/cli/utils/map.py
@@ -9,12 +9,12 @@
 import xarray as xr
 
 
-def make_map(base_dir, yyyy, mm, mapname):
+def make_map(path, yyyy, mm, mapname):
     # one map, per day, which collects the maximum extinction with no low-level clouds (<6km) at each station
-    with open(Path(base_dir) / yyyy / mm / mapname, 'w') as json_file:
+    with open(Path(path) / yyyy / mm / mapname, 'w') as json_file:
         json.dump({}, json_file)
 
-def add_to_map(fn, base_dir, yyyy, mm, dd, mapname):
+def add_to_map(fn, path, yyyy, mm, dd, mapname):
     # map collects the maximum extinction value with no low-level clouds (<6km) at each station at a hourly resolution
     # for each station, write an array with extinction values, and array with scenes for each hour of the day
     
@@ -51,7 +51,7 @@ def add_to_map(fn, base_dir, yyyy, mm, dd, mapname):
     mean_lidar_ratio = ds.lidar_ratio.resample(time='1h').mean().data
 
     # open current map
-    with open(Path(base_dir) / yyyy / mm / mapname, 'r') as json_file:
+    with open(Path(path) / yyyy / mm / mapname, 'r') as json_file:
         data = json.load(json_file)
     json_file.close()        
 
@@ -81,5 +81,5 @@ def add_to_map(fn, base_dir, yyyy, mm, dd, mapname):
     }
 
     # write new map
-    with open(Path(base_dir) / yyyy / mm / mapname, 'w') as json_file:
+    with open(Path(path) / yyyy / mm / mapname, 'w') as json_file:
         json.dump(data, json_file)

From 975140b192413fbc184e1edf3023d32ec5524e4a Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Wed, 9 Oct 2024 18:16:15 +0200
Subject: [PATCH 3/7] update documentation

---
 docs/cli.md | 82 ++++++++++++++++++++++++++---------------------------
 1 file changed, 41 insertions(+), 41 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 343f27b..27c4992 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -54,36 +54,36 @@ apro --help
 
 ```
 apro run --help
-                                                                                                                                       
- Usage: apro run [OPTIONS]                                                                                                             
-                                                                                                                                       
- run aprofiles standard workflow for given dates and specific instruments types                                                        
- see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)                                                           
-                                                                                                                                       
-╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --date                                             [%Y-%m-%d]              📅 Processing date.                                      │
-│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                         │
-│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]                │
-│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]             │
-│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]     │
-│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed.         │
-│                                                                            [default: CHM15k, Mini-MPL]                              │
-│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode.                             │
-│                                                                            [default: no-multiprocessing]                            │
-│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode i… │
-│                                                                            enabled).                                                │
-│                                                                            [env var: NSLOTS]                                        │
-│                                                                            [default: 2]                                             │
-│ --basedir-in                                       PATH                    📂 Base path for input data. [default: data/e-profile]   │
-│ --basedir-out                                      PATH                    📂 Base path for output data. [default: data/v-profiles] │
-│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file. [default: config] │
-│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                   │
-│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]            │
-│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                      │
-│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]      │
-│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]            │
-│ --help                                                                     Show this message and exit.                              │
-╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+                                                                                                                                        
+ Usage: apro run [OPTIONS]                                                                                                              
+                                                                                                                                        
+ run aprofiles standard workflow for given dates and specific instruments types                                                         
+ see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)                                                            
+                                                                                                                                        
+╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --date                                             [%Y-%m-%d]              📅 Processing date.                                       │
+│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                          │
+│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]                 │
+│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]              │
+│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]      │
+│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed.          │
+│                                                                            [default: CHM15k, Mini-MPL]                               │
+│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode.                              │
+│                                                                            [default: no-multiprocessing]                             │
+│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode is  │
+│                                                                            enabled).                                                 │
+│                                                                            [env var: NSLOTS]                                         │
+│                                                                            [default: 2]                                              │
+│ --path-in                                          PATH                    📂 Base path for input data. [default: data/e-profile]    │
+│ --path-out                                         PATH                    📂 Base path for output data. [default: data/v-profiles]  │
+│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file. [default: config]  │
+│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                    │
+│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]             │
+│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                       │
+│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]       │
+│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]             │
+│ --help                                                                     Show this message and exit.                               │
+╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 #### Examples
@@ -133,17 +133,17 @@ apro run --today --yesterday --multiprocessing
 
 ```
 apro l2b --help
-                                                                                                                                       
- Usage: apro l2b [OPTIONS]                                                                                                             
-                                                                                                                                       
- make E-PROFILE L2b files out of AP files                                                                                              
-                                                                                                                                       
-╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --basedir-in                           PATH  📂 Base path for input data. [default: data/v-profiles]                                │
-│ --basedir-out                          PATH  📂 Base path for output data. [default: data/l2b]                                      │
-│ --progress-bar    --no-progress-bar          ⌛ Show progress bar. [default: progress-bar]                                          │
-│ --help                                       Show this message and exit.                                                            │
-╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+                                                                                                                                        
+ Usage: apro l2b [OPTIONS]                                                                                                              
+                                                                                                                                        
+ make E-PROFILE L2b files out of AP files                                                                                               
+                                                                                                                                        
+╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --path-in                              PATH  📂 Base path for input data. [default: data/v-profiles]                                 │
+│ --path-out                             PATH  📂 Base path for output data. [default: data/l2b]                                       │
+│ --progress-bar    --no-progress-bar          ⌛ Show progress bar. [default: progress-bar]                                           │
+│ --help                                       Show this message and exit.                                                             │
+╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 #### Examples

From e66185b8f7552fe1cd559beea3ba055e3e664bee Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Wed, 9 Oct 2024 18:21:08 +0200
Subject: [PATCH 4/7] update documentation

---
 docs/cli.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 27c4992..7a3a696 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -19,21 +19,21 @@ required extras:
 
 :simple-pipx: via *pip/pipx*
 
-```
+``` bash
 pip install .[cli]
 ```
 
 :simple-poetry: via *poetry*
 
-```
+``` bash
 poetry install --extras cli
 ```
 
 ## Documentation
 
-`apro` commands which can be listed with
+`apro` commands can be listed with `apro --help`
 
-``` console
+``` bash
 apro --help
                                                                                                                                        
  Usage: apro [OPTIONS] COMMAND [ARGS]...                                                                                               
@@ -52,7 +52,7 @@ apro --help
 
 ### `run` command
 
-```
+``` bash
 apro run --help
                                                                                                                                         
  Usage: apro run [OPTIONS]                                                                                                              
@@ -90,19 +90,19 @@ apro run --help
 
 ##### run a specific date
 
-```
+``` bash
 apro run --date 2021-09-09
 ```
 
 ##### run today\'s files
 
-```
+``` bash
 apro run --today
 ```
 
 ##### run yesterday\'s files
 
-```
+``` bash
 apro run --yesterday
 ```
 
@@ -110,13 +110,13 @@ It is possible to combine different options.
 
 ##### run today\'s and yesterday\'s files for CHM15k only
 
-```
+``` bash
 apro run --today --yesterday --instruments-type CHM15k
 ```
 
 ##### update only calendar files for 2021
 
-```
+``` bash
 apro run --from 2021-01-01 --to 2021-12-31 --no-update-data --no-update-map
 ```
 
@@ -124,14 +124,14 @@ apro run --from 2021-01-01 --to 2021-12-31 --no-update-data --no-update-map
 
 The data processing can be run in parallel by using the
 [`multiprocessing`] option :
-```
+``` bash
 apro run --today --yesterday --multiprocessing
 ```
 
 
 ### `l2b` command
 
-```
+``` bash
 apro l2b --help
                                                                                                                                         
  Usage: apro l2b [OPTIONS]                                                                                                              

From 87df97b0ffb5e8b0ee8d3e55da1fedd6066e74c9 Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Thu, 10 Oct 2024 08:55:41 +0200
Subject: [PATCH 5/7] edit L2B file names

---
 aprofiles/cli/utils/l2b.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/aprofiles/cli/utils/l2b.py b/aprofiles/cli/utils/l2b.py
index 97ccd1a..7a7ca64 100644
--- a/aprofiles/cli/utils/l2b.py
+++ b/aprofiles/cli/utils/l2b.py
@@ -31,7 +31,7 @@ def make_files(path_in: Path, path_out: Path, progress_bar: bool) -> None:
         for i in myrange:
             ds1t = ds.isel(time=i)
             mmhh = pd.to_datetime(ds1t.time.data).strftime('%H%M')
-            file_name = Path(path_out, f"{unique_id}_{yyyymmdd}{mmhh}.nc")
+            file_name = Path(path_out, f"L2B_{unique_id}{yyyymmdd}{mmhh}.nc")
             ds1t.to_netcdf('out.nc')
             os.rename('out.nc',file_name)
 

From 7139820ecfa343fa60ecb82d5294c81adb36dae3 Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Thu, 10 Oct 2024 09:22:51 +0200
Subject: [PATCH 6/7] update documentation

---
 aprofiles/cli/apro.py      |   5 +-
 aprofiles/cli/utils/l2b.py |  18 ++----
 docs/cli.md                | 109 +++++++++++++++++++------------------
 3 files changed, 66 insertions(+), 66 deletions(-)

diff --git a/aprofiles/cli/apro.py b/aprofiles/cli/apro.py
index 35800f8..eb6947d 100755
--- a/aprofiles/cli/apro.py
+++ b/aprofiles/cli/apro.py
@@ -200,6 +200,9 @@ def l2b(
         path_out: Path = typer.Option(
             "data/l2b", exists=True, writable=True, help="📂 Base path for output data."
         ),
+        time_steps: int = typer.Option(
+            12, help="🔂 Number of most recent time steps to be processed."
+        ),
         progress_bar: bool = typer.Option(True, help="⌛ Show progress bar.")
     ):
     """
@@ -212,7 +215,7 @@ def l2b(
         today = datetime.today()
         path_in = Path(path_in, today.strftime('%Y'), today.strftime('%m'), today.strftime('%d'))
     
-    utils.l2b.make_files(path_in, path_out, progress_bar)
+    utils.l2b.make_files(path_in, path_out, time_steps, progress_bar)
 
 if __name__ == "__main__":
     app()
diff --git a/aprofiles/cli/utils/l2b.py b/aprofiles/cli/utils/l2b.py
index 7a7ca64..b7c7286 100644
--- a/aprofiles/cli/utils/l2b.py
+++ b/aprofiles/cli/utils/l2b.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 import os
 import sys
 from pathlib import Path
@@ -10,29 +9,24 @@
 import pandas as pd
 from rich.progress import track
 
-def make_files(path_in: Path, path_out: Path, progress_bar: bool) -> None:
+def make_files(path_in: Path, path_out: Path, time_steps: int, progress_bar: bool) -> None:
     
     # list all AP files in path_in
-    files = glob(f"{path_in}/AP*nc")
+    files = list(Path(path_in).glob("AP*nc"))
 
     for f in track(files, description=f"Reading AP files", disable=not progress_bar):
 
-        ds = xr.open_dataset(f, decode_times=True, chunks=-1).load()
+        ds = xr.open_dataset(f, decode_times=True, chunks=-1)
         # get unique id and extract yyyymmdd from first time step
         unique_id = f"{ds.attrs['wigos_station_id']}_{ds.attrs['instrument_id']}"
         yyyymmdd = str(ds.time.data[0].astype('M8[D]')).replace('-','')        
         
-        ntimes = ds.time.size
-        if ntimes < 60:
-            myrange = range(ntimes)
-        else:
-            myrange = range(ntimes-12, ntimes)
+        # we just work with n latest time steps
+        start_idx = max(0, ds.time.size - time_steps)
 
-        for i in myrange:
+        for i in range(start_idx, ds.time.size):
             ds1t = ds.isel(time=i)
             mmhh = pd.to_datetime(ds1t.time.data).strftime('%H%M')
             file_name = Path(path_out, f"L2B_{unique_id}{yyyymmdd}{mmhh}.nc")
             ds1t.to_netcdf('out.nc')
             os.rename('out.nc',file_name)
-
-
diff --git a/docs/cli.md b/docs/cli.md
index 7a3a696..f5c221d 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -35,18 +35,18 @@ poetry install --extras cli
 
 ``` bash
 apro --help
-                                                                                                                                       
- Usage: apro [OPTIONS] COMMAND [ARGS]...                                                                                               
-                                                                                                                                       
-╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --install-completion          Install completion for the current shell.                                                             │
-│ --show-completion             Show completion for the current shell, to copy it or customize the installation.                      │
-│ --help                        Show this message and exit.                                                                           │
-╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
-╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ l2b   make E-PROFILE L2b files out of AP files                                                                                      │
-│ run   run aprofiles standard workflow for given dates and specific instruments types                                                │
-╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+                                                                                                                                     
+ Usage: apro [OPTIONS] COMMAND [ARGS]...                                                                                             
+                                                                                                                                     
+╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --install-completion          Install completion for the current shell.                                                           │
+│ --show-completion             Show completion for the current shell, to copy it or customize the installation.                    │
+│ --help                        Show this message and exit.                                                                         │
+╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Commands ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ l2b   make E-PROFILE L2b files out of AP files                                                                                    │
+│ run   run aprofiles standard workflow for given dates and specific instruments types                                              │
+╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 
@@ -54,36 +54,38 @@ apro --help
 
 ``` bash
 apro run --help
-                                                                                                                                        
- Usage: apro run [OPTIONS]                                                                                                              
-                                                                                                                                        
- run aprofiles standard workflow for given dates and specific instruments types                                                         
- see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)                                                            
-                                                                                                                                        
-╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --date                                             [%Y-%m-%d]              📅 Processing date.                                       │
-│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                          │
-│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]                 │
-│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]              │
-│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]      │
-│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed.          │
-│                                                                            [default: CHM15k, Mini-MPL]                               │
-│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode.                              │
-│                                                                            [default: no-multiprocessing]                             │
-│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode is  │
-│                                                                            enabled).                                                 │
-│                                                                            [env var: NSLOTS]                                         │
-│                                                                            [default: 2]                                              │
-│ --path-in                                          PATH                    📂 Base path for input data. [default: data/e-profile]    │
-│ --path-out                                         PATH                    📂 Base path for output data. [default: data/v-profiles]  │
-│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file. [default: config]  │
-│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                    │
-│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]             │
-│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                       │
-│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]       │
-│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]             │
-│ --help                                                                     Show this message and exit.                               │
-╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+                                                                                                                                     
+ Usage: apro run [OPTIONS]                                                                                                           
+                                                                                                                                     
+ run aprofiles standard workflow for given dates and specific instruments types                                                      
+ see some examples [here](https://augustinmortier.github.io/a-profiles/cli/)                                                         
+                                                                                                                                     
+╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --date                                             [%Y-%m-%d]              📅 Processing date.                                    │
+│ --from                                             [%Y-%m-%d]              📅 Initial date. [default: None]                       │
+│ --to                                               [%Y-%m-%d]              📅 Ending date. [default: (Today's date)]              │
+│ --today                 --no-today                                         🕑 Process today's data. [default: no-today]           │
+│ --yesterday             --no-yesterday                                     🕙 Process yesterday's data. [default: no-yesterday]   │
+│ --instruments-type                                 [CHM15k|Mini-MPL|CL61]  📗 List of specific instruments to be processed.       │
+│                                                                            [default: CHM15k, Mini-MPL]                            │
+│ --multiprocessing       --no-multiprocessing                               🚀 Use multiprocessing mode.                           │
+│                                                                            [default: no-multiprocessing]                          │
+│ --workers                                          INTEGER RANGE [x>=1]    👷 Number of workers (NSLOTS, if multiprocessing mode  │
+│                                                                            is enabled).                                           │
+│                                                                            [env var: NSLOTS]                                      │
+│                                                                            [default: 2]                                           │
+│ --path-in                                          PATH                    📂 Base path for input data. [default: data/e-profile] │
+│ --path-out                                         PATH                    📂 Base path for output data.                          │
+│                                                                            [default: data/v-profiles]                             │
+│ --apriori-cfg                                      PATH                    📂 Base path for a priori config file.                 │
+│                                                                            [default: config]                                      │
+│ --update-data           --no-update-data                                   📈 Update data. [default: update-data]                 │
+│ --update-calendar       --no-update-calendar                               🗓️ Update calendar. [default: update-calendar]          │
+│ --update-map            --no-update-map                                    🗺️ Update map. [default: update-map]                    │
+│ --update-climatology    --no-update-climatology                            ↪️ Update climatology. [default: update-climatology]    │
+│ --progress-bar          --no-progress-bar                                  ⌛ Show progress bar. [default: progress-bar]          │
+│ --help                                                                     Show this message and exit.                            │
+╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 #### Examples
@@ -133,17 +135,18 @@ apro run --today --yesterday --multiprocessing
 
 ``` bash
 apro l2b --help
-                                                                                                                                        
- Usage: apro l2b [OPTIONS]                                                                                                              
-                                                                                                                                        
- make E-PROFILE L2b files out of AP files                                                                                               
-                                                                                                                                        
-╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --path-in                              PATH  📂 Base path for input data. [default: data/v-profiles]                                 │
-│ --path-out                             PATH  📂 Base path for output data. [default: data/l2b]                                       │
-│ --progress-bar    --no-progress-bar          ⌛ Show progress bar. [default: progress-bar]                                           │
-│ --help                                       Show this message and exit.                                                             │
-╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+                                                                                                                                     
+ Usage: apro l2b [OPTIONS]                                                                                                           
+                                                                                                                                     
+ make E-PROFILE L2b files out of AP files                                                                                            
+                                                                                                                                     
+╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --path-in                              PATH     📂 Base path for input data. [default: data/v-profiles]                           │
+│ --path-out                             PATH     📂 Base path for output data. [default: data/l2b]                                 │
+│ --time-steps                           INTEGER  🔂 Number of most recent time steps to be processed. [default: 12]                │
+│ --progress-bar    --no-progress-bar             ⌛ Show progress bar. [default: progress-bar]                                     │
+│ --help                                          Show this message and exit.                                                       │
+╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 #### Examples

From 85233f1b169ccf36c1957cd3f6279d71fe9f61ab Mon Sep 17 00:00:00 2001
From: augustinm <augustinm@met.no>
Date: Thu, 10 Oct 2024 09:25:11 +0200
Subject: [PATCH 7/7] update documentation

---
 docs/changelog.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 0146cf2..c47a5ba 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -7,7 +7,7 @@ Oct 10, 2024
 
 - revisit CLI: two commands
     - `apro run` (formerly `aprocess`: run standard workflow)
-    - `apro l2b` (creates L2b files out of AP files)
+    - `apro l2b` (creates L2B files out of AP files)
 
 ## 0.9.7
 Oct 3, 2024