Merge pull request nf-core#2459 from mashehu/fix-linting-report-links

fix incorrect links in github linting comment

.github/CONTRIBUTING.md

@@ -92,7 +92,7 @@ pre-commit run --all
 ## API Documentation
 
 We aim to write function docstrings according to the [Google Python style-guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings). These are used to automatically generate package documentation on the nf-core website using Sphinx.
-You can find this documentation here: [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
+You can find this documentation here: [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/)
 
 If you would like to test the documentation, you can install Sphinx locally by following Sphinx's [installation instruction](https://www.sphinx-doc.org/en/master/usage/installation.html).
 Once done, you can run `make clean` and then `make html` in the `docs/api` directory of `nf-core tools`.

README.md

@@ -57,7 +57,7 @@ A python package with helper tools for the nf-core community.
 - [Citation](#citation)
 
 The nf-core tools package is written in Python and can be imported and used within other packages.
-For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/).
+For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools/docs/).
 
 ## Installation
 
@@ -186,7 +186,7 @@ for wf in wfs.remote_workflows:
     print(wf.full_name)
 ```
 
-Please see [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/) for the function documentation.
+Please see [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/) for the function documentation.
 
 ### Automatic version check
 
@@ -533,7 +533,7 @@ Each test result name on the left is a terminal hyperlink.
 In most terminals you can <kbd>ctrl</kbd> + <kbd>click</kbd> ( <kbd>cmd</kbd> + <kbd>click</kbd>) these
 links to open documentation specific to this test in your browser.
 
-Alternatively visit <https://nf-co.re/tools-docs/lint_tests/index.html> and find your test to read more.
+Alternatively visit <https://nf-co.re/tools/docs/latest/pipeline_lint_tests/index.html> and find your test to read more.
 
 ### Linting config
 

nf_core/__main__.py

@@ -448,7 +448,7 @@ def lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, ma
 
     Runs a large number of automated tests to ensure that the supplied pipeline
     meets the nf-core guidelines. Documentation of all lint tests can be found
-    on the nf-core website: [link=https://nf-co.re/tools-docs/]https://nf-co.re/tools-docs/[/]
+    on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/]
 
     You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/].
     See the documentation for details.

nf_core/lint/__init__.py

@@ -371,10 +371,10 @@ def format_result(test_results):
             Given an list of error message IDs and the message texts, return a nicely formatted
             string for the terminal with appropriate ASCII colours.
             """
+            tools_version = __version__
+            if "dev" in __version__:
+                tools_version = "latest"
             for eid, msg in test_results:
-                tools_version = __version__
-                if "dev" in __version__:
-                    tools_version = "latest"
                 yield Markdown(
                     f"[{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html): {msg}"
                 )
@@ -466,6 +466,10 @@ def _get_results_md(self):
         if len(self.failed) > 0:
             overall_result = "Failed :x:"
 
+        tools_version = __version__
+        if "dev" in __version__:
+            tools_version = "latest"
+
         # List of tests for details
         test_failure_count = ""
         test_failures = ""
@@ -474,7 +478,7 @@ def _get_results_md(self):
             test_failures = "### :x: Test failures:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.failed
                     ]
@@ -488,7 +492,7 @@ def _get_results_md(self):
             test_ignored = "### :grey_question: Tests ignored:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.ignored
                     ]
@@ -502,7 +506,7 @@ def _get_results_md(self):
             test_fixed = "### :grey_question: Tests fixed:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.fixed
                     ]
@@ -516,7 +520,7 @@ def _get_results_md(self):
             test_warnings = "### :heavy_exclamation_mark: Test warnings:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.warned
                     ]
@@ -531,7 +535,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         (
-                            f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html)"
+                            f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html)"
                             f" - {strip_ansi_codes(msg, '`')}"
                         )
                         for eid, msg in self.passed