From 4d2f521049ae26a6a601ceb10ddb6c26ae0bc11c Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 24 Mar 2021 19:42:59 +0100 Subject: [PATCH 1/3] tweak TODO string in test_yml_builder.py --- nf_core/modules/test_yml_builder.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/modules/test_yml_builder.py b/nf_core/modules/test_yml_builder.py index b5e22795c6..0abb5cd719 100644 --- a/nf_core/modules/test_yml_builder.py +++ b/nf_core/modules/test_yml_builder.py @@ -243,7 +243,7 @@ def get_md5_sums(self, entry_point, command): test_files[i].pop("md5sum") test_files[i][ "contains" - ] = "# TODO nf-core: md5sum test not possible, please replace this comment with a string in the file" + ] = "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead" if len(test_files) == 0: raise UserWarning(f"Could not find any test result files in '{results_dir}'") From 67a5994dd7ef62658633f2294bcca3ca9cc8adfd Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 24 Mar 2021 19:45:36 +0100 Subject: [PATCH 2/3] tweak log output in bioconda package name prompt --- nf_core/modules/create.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py index 4d9aae79cd..6f1f0cbde4 100644 --- a/nf_core/modules/create.py +++ b/nf_core/modules/create.py @@ -138,10 +138,11 @@ def create(self): log.info(f"Using Bioconda package: '{self.bioconda}'") break except (ValueError, LookupError) as e: + log.warning(f"Could not find Conda dependency using the Anaconda API: '{self.tool}'") if rich.prompt.Confirm.ask( - f"[violet]Could not find Conda dependency using the Anaconda API: '{self.tool}'. Do you want to enter a different bioconda package name?" + f"[violet]Do you want to enter a different Bioconda package name?" ): - self.tool_conda_name = rich.prompt.Prompt.ask("[violet]Name of tool/subtool").strip() + self.tool_conda_name = rich.prompt.Prompt.ask("[violet]Name of Bioconda package").strip() continue else: log.warning( From f666c0500370cec02d7bb46bbf49a7d98ef10cf6 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 24 Mar 2021 20:01:54 +0100 Subject: [PATCH 3/3] Black --- nf_core/modules/create.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py index 6f1f0cbde4..ed7f778bfc 100644 --- a/nf_core/modules/create.py +++ b/nf_core/modules/create.py @@ -139,9 +139,7 @@ def create(self): break except (ValueError, LookupError) as e: log.warning(f"Could not find Conda dependency using the Anaconda API: '{self.tool}'") - if rich.prompt.Confirm.ask( - f"[violet]Do you want to enter a different Bioconda package name?" - ): + if rich.prompt.Confirm.ask(f"[violet]Do you want to enter a different Bioconda package name?"): self.tool_conda_name = rich.prompt.Prompt.ask("[violet]Name of Bioconda package").strip() continue else: