From 0397288a84ef1a00736f2d6c5d1c3fd0a212b7c7 Mon Sep 17 00:00:00 2001
From: johaGL <johanna.galvis@ibgc.cnrs.fr>
Date: Fri, 26 Jan 2024 15:57:14 +0100
Subject: [PATCH] fix(help menu): hydra guided, deleted click usage

---
 src/dimet/__main__.py                       | 24 ++++++-------
 src/dimet/config/config.yaml                | 13 +++----
 src/dimet/config/hydra/help/dimet_help.yaml | 38 +++++++++++++++++++++
 3 files changed, 56 insertions(+), 19 deletions(-)
 create mode 100644 src/dimet/config/hydra/help/dimet_help.yaml

diff --git a/src/dimet/__main__.py b/src/dimet/__main__.py
index 47ba33e..516302b 100644
--- a/src/dimet/__main__.py
+++ b/src/dimet/__main__.py
@@ -9,12 +9,11 @@
 
 import hydra
 
-from dimet.method import Method
 from omegaconf import DictConfig, OmegaConf
 
 from dimet.data import Dataset
+from dimet.method import Method
 
-import click
 
 logger = logging.getLogger(__name__)
 
@@ -34,18 +33,17 @@ def main_run_analysis(cfg: DictConfig) -> None:
     method.run(cfg, dataset)
 
 
-@click.command(context_settings=dict(
-        help_option_names=['-h', '--help'])  # needed to recognize -h as well
+def fully_empty_args_custom_message() -> None:
+    custom_message: str = (
+        "\nDIMet is a tool for the Differential analysis of "
+        "targeted Isotope-labeled Metabolomics data. \n\n  Please type "
+        "'python -m dimet --help' or 'python -m dimet -h' for usage.\n"
     )
-@click.option('-cd', type=str, required=True,
-              help="Directory containing the general configuration "
-                   "(see -cn)")
-@click.option('-cn', type=str, required=True,
-              help="File name of the general configuration "
-                   "(only one .yaml file name)")
-def main_run_analysis__or_display_help(cd, cn) -> None:
-    main_run_analysis()  # run: hydra handles further arguments validation
+    print(custom_message)
 
 
 if __name__ == "__main__":
-    main_run_analysis__or_display_help()
+    if len(sys.argv) <= 1:
+        fully_empty_args_custom_message()
+    else:
+        main_run_analysis()
diff --git a/src/dimet/config/config.yaml b/src/dimet/config/config.yaml
index a338f1d..a924851 100644
--- a/src/dimet/config/config.yaml
+++ b/src/dimet/config/config.yaml
@@ -3,16 +3,17 @@ hydra:
     chdir: true
   run:
     dir: ../outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}/${analysis.dataset.label}-${analysis.method.label}
-    
-# Notes: 
-# This config.yaml file is never used by the code, but remains here as template.
-# All the method/*.yaml files YES THEY ARE USED by the code
+
+
+# This config.yaml file is used by the code when calling --help
 
 defaults:
-  - analysis: abundance_plot
+  # - analysis: abundance_plot  # deactivated as it blocks the --help display
   - _self_
+  - override hydra/help: dimet_help
+
 
 figure_path: figures
 table_path: tables
 
-# check https://hydra.cc/docs/patterns/specializing_config/ for more info about this
+# check https://hydra.cc/docs/patterns/specializing_config/ for more info about this
\ No newline at end of file
diff --git a/src/dimet/config/hydra/help/dimet_help.yaml b/src/dimet/config/hydra/help/dimet_help.yaml
new file mode 100644
index 0000000..af72056
--- /dev/null
+++ b/src/dimet/config/hydra/help/dimet_help.yaml
@@ -0,0 +1,38 @@
+# App name, override to match the name your app is known by
+app_name: DIMet
+
+# Help header, customize to describe your app to your users
+header: Welcome to ${hydra.help.app_name}!
+
+footer: |-
+  Powered by Hydra (https://hydra.cc)
+  Use --hydra-help to view Hydra specific help
+
+template: |-
+  ${hydra.help.header}
+
+  DIMet is a tool for the Differential analysis of targeted Isotope-labeled Metabolomics data
+  
+  Usage: python -m dimet [options]
+
+  optional arguments:
+    -cd, --config-dir     Directory name where the general configuration is located (see -cn)
+    -cn, --config-name    File name of the general configuration, only one .yaml file name
+    -h, --help            Show this help message and exit
+  
+  
+  == Available analyses ==
+  $APP_CONFIG_GROUPS
+ 
+  ${hydra.help.footer}
+  
+
+# Basic Hydra flags:
+#   $FLAGS_HELP
+#
+# Config groups, choose one of:
+#   $APP_CONFIG_GROUPS: All config groups that does not start with hydra/.
+#   $HYDRA_CONFIG_GROUPS: All the Hydra config groups (starts with hydra/)
+#
+# Configuration generated with overrides:
+#   $CONFIG : Generated config