From 42c467d33cdf2adecf652dcaa359e3a72e947018 Mon Sep 17 00:00:00 2001
From: Matteo Fiandesio <matteo.fiandesio@seqera.io>
Date: Mon, 18 Mar 2024 16:43:41 +0100
Subject: [PATCH 1/7] fix: adds a short sha representation to modules list
command pointing to the repo specific commit
---
nf_core/components/list.py | 7 ++++---
nf_core/modules/modules_repo.py | 8 ++++++++
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index b0c5af219f..f4407285cd 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -125,10 +125,11 @@ def pattern_msg(keywords: List[str]) -> str:
version_sha = component_entry["git_sha"]
try:
# pass repo_name to get info on modules even outside nf-core/modules
- message, date = ModulesRepo(
+ module = ModulesRepo(
remote_url=repo_url,
branch=component_entry["branch"],
- ).get_commit_info(version_sha)
+ )
+ message, date = module.get_commit_info(version_sha)
except LookupError as e:
log.warning(e)
date = "[red]Not Available"
@@ -140,7 +141,7 @@ def pattern_msg(keywords: List[str]) -> str:
version_sha = "[red]Not Available"
date = "[red]Not Available"
message = "[red]Not Available"
- table.add_row(component, repo_url, version_sha, message, date)
+ table.add_row(component, f'[link={repo_url}]{repo_url}[/link]', f'[link={module.gitless_repo()}/commit/{version_sha}]{version_sha[:7]}[/link]', message, date)
components.append(component)
if print_json:
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 204c20fd71..7f58641aa6 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -69,6 +69,14 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
self.avail_module_names = None
+
+ def gitless_repo(self):
+ gitless_repo_url = self.remote_url
+ if(self.remote_url and '.git' in self.remote_url):
+ gitless_repo_url = gitless_repo_url[:-3]
+ return gitless_repo_url
+
+
def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
"""
Sets up the local git repository. If the repository has been cloned previously, it
From ca5b78b675b46fc474eb1f494b25fd0c288958ed Mon Sep 17 00:00:00 2001
From: Matteo Fiandesio <matteo.fiandesio@seqera.io>
Date: Mon, 18 Mar 2024 17:32:58 +0100
Subject: [PATCH 2/7] adds changelog entry
---
CHANGELOG.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e3189edaa..3fb06f4509 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,7 @@
- Patch: handle file not found when it is an added file to a module ([#2771](https://github.com/nf-core/tools/pull/2771))
- Handle symlinks when migrating pytest ([#2770](https://github.com/nf-core/tools/pull/2770))
- Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
+- Reduce the size of the sha representation in the `list` command and links to the specific commit ([#2870](https://github.com/nf-core/tools/pull/2870))
### General
From 171914b538c1b746454bf2bac6e1e7651f8d3a37 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 18 Mar 2024 21:04:57 +0000
Subject: [PATCH 3/7] [automated] Fix code linting
---
nf_core/components/list.py | 8 +++++++-
nf_core/modules/modules_repo.py | 4 +---
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index f4407285cd..1606cfe74a 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -141,7 +141,13 @@ def pattern_msg(keywords: List[str]) -> str:
version_sha = "[red]Not Available"
date = "[red]Not Available"
message = "[red]Not Available"
- table.add_row(component, f'[link={repo_url}]{repo_url}[/link]', f'[link={module.gitless_repo()}/commit/{version_sha}]{version_sha[:7]}[/link]', message, date)
+ table.add_row(
+ component,
+ f"[link={repo_url}]{repo_url}[/link]",
+ f"[link={module.gitless_repo()}/commit/{version_sha}]{version_sha[:7]}[/link]",
+ message,
+ date,
+ )
components.append(component)
if print_json:
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 7f58641aa6..839f2a75ee 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -69,14 +69,12 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
self.avail_module_names = None
-
def gitless_repo(self):
gitless_repo_url = self.remote_url
- if(self.remote_url and '.git' in self.remote_url):
+ if self.remote_url and ".git" in self.remote_url:
gitless_repo_url = gitless_repo_url[:-3]
return gitless_repo_url
-
def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
"""
Sets up the local git repository. If the repository has been cloned previously, it
From afaf2ff826eb039a7751d7e29b90a52b6c07f4b9 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 18 Mar 2024 22:43:32 +0100
Subject: [PATCH 4/7] Hyperlink module name and file path in lint results
---
nf_core/components/lint/__init__.py | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index c99934bca3..ee1bd58b15 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -11,6 +11,7 @@
import rich.box
import rich.console
import rich.panel
+import rich.repr
from rich.markdown import Markdown
from rich.table import Table
@@ -31,6 +32,7 @@ class LintExceptionError(Exception):
pass
+@rich.repr.auto
class LintResult:
"""An object to hold the results of a lint test"""
@@ -42,6 +44,7 @@ def __init__(self, component, lint_test, message, file_path):
self.component_name = component.component_name
+@rich.repr.auto
class ComponentLint(ComponentCommand):
"""
An object for linting modules and subworkflows either in a clone of the 'nf-core/modules'
@@ -231,9 +234,20 @@ def format_result(test_results, table):
if last_modname and lint_result.component_name != last_modname:
even_row = not even_row
last_modname = lint_result.component_name
+
+ # If this is an nf-core module, link to the nf-core webpage
+ if lint_result.component.repo_url == "https://github.com/nf-core/modules.git":
+ module_name = f"[link=https://nf-co.re/modules/{lint_result.component_name.replace("/","_")}]{lint_result.component_name}[/link]"
+ else:
+ module_name = lint_result.component_name
+
+ # Make the filename clickable to open in VSCode
+ file_path = os.path.relpath(lint_result.file_path, self.dir)
+ file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]"
+
table.add_row(
- Markdown(f"{lint_result.component_name}"),
- os.path.relpath(lint_result.file_path, self.dir),
+ module_name,
+ file_path_link,
Markdown(f"{lint_result.message}"),
style="dim" if even_row else None,
)
From fba35785979eb713480f81446fff231ab142d104 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 18 Mar 2024 22:51:06 +0100
Subject: [PATCH 5/7] Fix link and shorten GitHub repo name in nf-core modules
list local
---
nf_core/components/list.py | 5 +++--
nf_core/modules/modules_repo.py | 2 +-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index 1606cfe74a..f5f2744e17 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -70,7 +70,7 @@ def pattern_msg(keywords: List[str]) -> str:
# We have a pipeline - list what's installed
else:
# Check that we are in a pipeline directory
- print(f"{self.repo_type=}")
+ log.info(f"Repository type: [blue]{self.repo_type}")
try:
if self.repo_type != "pipeline":
raise UserWarning(
@@ -141,9 +141,10 @@ def pattern_msg(keywords: List[str]) -> str:
version_sha = "[red]Not Available"
date = "[red]Not Available"
message = "[red]Not Available"
+ nice_repo_name = repo_url.replace("https://github.com/", "").replace(".git", "")
table.add_row(
component,
- f"[link={repo_url}]{repo_url}[/link]",
+ f"[link={repo_url}]{nice_repo_name}[/link]",
f"[link={module.gitless_repo()}/commit/{version_sha}]{version_sha[:7]}[/link]",
message,
date,
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 839f2a75ee..9694920274 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -72,7 +72,7 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
def gitless_repo(self):
gitless_repo_url = self.remote_url
if self.remote_url and ".git" in self.remote_url:
- gitless_repo_url = gitless_repo_url[:-3]
+ gitless_repo_url = gitless_repo_url[:-4]
return gitless_repo_url
def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
From 554d5d719b5851a017b38e601ab7039625d04fce Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 18 Mar 2024 22:52:50 +0100
Subject: [PATCH 6/7] extend changelog
---
CHANGELOG.md | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e51597e89c..1e84fc8043 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -79,7 +79,8 @@
- Patch: handle file not found when it is an added file to a module ([#2771](https://github.com/nf-core/tools/pull/2771))
- Handle symlinks when migrating pytest ([#2770](https://github.com/nf-core/tools/pull/2770))
- Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
-- Reduce the size of the sha representation in the `list` command and links to the specific commit ([#2870](https://github.com/nf-core/tools/pull/2870))
+- Reduce the sha length in the `nf-core modules list local` and add links to the specific commit ([#2870](https://github.com/nf-core/tools/pull/2870))
+- Add links the nf-core module page and to open the local file in VSCode for module lint results ([#2870](https://github.com/nf-core/tools/pull/2870))
### General
From 54afd8d54c8523715dd3e9475574407a903f46d1 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Mon, 18 Mar 2024 23:00:50 +0100
Subject: [PATCH 7/7] Try to fix linting
---
nf_core/components/lint/__init__.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index ee1bd58b15..564dcfaf6b 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -237,7 +237,8 @@ def format_result(test_results, table):
# If this is an nf-core module, link to the nf-core webpage
if lint_result.component.repo_url == "https://github.com/nf-core/modules.git":
- module_name = f"[link=https://nf-co.re/modules/{lint_result.component_name.replace("/","_")}]{lint_result.component_name}[/link]"
+ module_url = "https://nf-co.re/modules/" + lint_result.component_name.replace("/", "_")
+ module_name = f"[link={module_url}]{lint_result.component_name}[/link]"
else:
module_name = lint_result.component_name