From 10e46353784740908af95283ebe51cc8ac1a1fee Mon Sep 17 00:00:00 2001 From: nlouwen Date: Fri, 25 Oct 2024 14:46:29 +0200 Subject: [PATCH] amend db only and no trees help text --- big_scape/cli/cli_common_options.py | 6 ++++-- big_scape/output/legacy_output.py | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/big_scape/cli/cli_common_options.py b/big_scape/cli/cli_common_options.py index 4f23bfb1..514205d8 100644 --- a/big_scape/cli/cli_common_options.py +++ b/big_scape/cli/cli_common_options.py @@ -118,7 +118,8 @@ def common_all(fn): is_flag=True, default=False, help="Do not generate any output besides the data stored in the database. " - "Suitable for advanced users that work with the SQL database directly.", + "Suitable for advanced users that wish to only make use of the results " + "stored in the SQLite database.", ), click.option( "--no-trees", @@ -126,7 +127,8 @@ def common_all(fn): is_flag=True, default=False, help="Do not generate any GCF newick trees. Suitable for users that do not " - "utilize our output visualization, but work with output tsv files directly.", + "utilize our output visualization, but only make use of the output stored " + "in the tsv files and/or SQLite database.", ), click.option( "--force-gbk", diff --git a/big_scape/output/legacy_output.py b/big_scape/output/legacy_output.py index b33b9262..b1389e80 100644 --- a/big_scape/output/legacy_output.py +++ b/big_scape/output/legacy_output.py @@ -164,7 +164,7 @@ def legacy_prepare_output( click_context = click.get_current_context(silent=True) if click_context and click_context.obj["db_only_output"]: - logging.info("Skipping all output generation") + logging.info("Skipping all (non-SQLite db related) output generation") return copy_base_output_templates(output_dir)