From b96f56b15d24431fb97382bed7715bccfafd21df Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 31 May 2024 23:35:39 +0200 Subject: [PATCH 1/2] Conda module linting: Include package name in log file MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Tried to do this with GitHub Copilot Workspaces but it failed 😅 As I was looking at the code anyway I could see the fix so figured I would put it manually. Closes https://github.com/nf-core/tools/issues/3009 Untested, done in web browser only. --- nf_core/modules/lint/main_nf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index fd4d81f7f2..81308ba5c5 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -367,14 +367,14 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): # response = _bioconda_package(bp) response = nf_core.utils.anaconda_package(bp) except LookupError: - self.warned.append(("bioconda_version", "Conda version not specified correctly", self.main_nf)) + self.warned.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)) except ValueError: - self.failed.append(("bioconda_version", "Conda version not specified correctly", self.main_nf)) + self.failed.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)) else: # Check that required version is available at all if bioconda_version not in response.get("versions"): self.failed.append( - ("bioconda_version", f"Conda package had unknown version: `{bioconda_version}`", self.main_nf) + ("bioconda_version", f"Conda package {bp} had unknown version: `{bioconda_version}`", self.main_nf) ) continue # No need to test for latest version, continue linting # Check version is latest available From 847a3763d1b67a9e75432bf0c74a0c531891d687 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 3 Jun 2024 08:40:07 +0000 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1d7678c45..6b421ba4de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ ### Linting - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) +- Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) ### Download