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Bugfix tweaks #947

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Merged
ewels merged 5 commits into from
Mar 23, 2021
+16 −10
Merged

Bugfix tweaks #947

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7a1c333
Copy file if any exception with jinja in pipeline create
ewels Mar 23, 2021
719d22d
Make lint summary table coloured according to overall status
ewels Mar 23, 2021
6084456
Changelog
ewels Mar 23, 2021
b7bd4c4
Merge branch 'dev' into bugfix-tweaks
ewels Mar 23, 2021
17fbcf8
Use '21.03.0-edge' in bump-versions code
ewels Mar 23, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
* Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
* Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
* Added automated PR comments to the Markdown, YAML and Python lint CI tests to explain failures (tools and pipeline template)
* Make `nf-core lint` summary table borders coloured according to overall pass / fail status

## [v1.13.1 - Copper Crocodile Patch :crocodile: :pirate_flag:](https://github.com/nf-core/tools/releases/tag/1.13.1) - [2021-03-19]

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4 changes: 2 additions & 2 deletions nf_core/bump_version.py
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Expand Up @@ -145,8 +145,8 @@ def bump_nextflow_version(pipeline_obj, new_version):
pipeline_obj,
[
(
r"nxf_ver: \[[\'\"]?{}[\'\"]?, ''\]".format(current_version.replace(".", r"\.")),
"nxf_ver: ['{}', '']".format(new_version),
r"nxf_ver: \[[\'\"]?{}[\'\"]?, '21.03.0-edge'\]".format(current_version.replace(".", r"\.")),
"nxf_ver: ['{}', '21.03.0-edge']".format(new_version),
)
],
)
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6 changes: 5 additions & 1 deletion nf_core/create.py
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Expand Up @@ -132,7 +132,11 @@ def render_template(self):
except (AttributeError, UnicodeDecodeError) as e:
log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
shutil.copy(template_fn_path, output_path)
continue

# Something else went wrong
except Exception as e:
log.error(f"Copying raw file as error rendering with Jinja: '{output_path}' - {e}")
shutil.copy(template_fn_path, output_path)

# Mirror file permissions
template_stat = os.stat(template_fn_path)
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15 changes: 8 additions & 7 deletions nf_core/lint/__init__.py
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Expand Up @@ -318,14 +318,15 @@ def _s(some_list):
console.print(table)

# Summary table
table = Table(box=rich.box.ROUNDED)
table.add_column("[bold green]LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)
table.add_row(r"[✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)), style="green")
summary_colour = "red" if len(self.failed) > 0 else "green"
table = Table(box=rich.box.ROUNDED, style=summary_colour)
table.add_column(f"LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)
table.add_row(r"[green][✔] {:>3} Test{} Passed".format(len(self.passed), _s(self.passed)))
if len(self.fix):
table.add_row(r"[?] {:>3} Test{} Fixed".format(len(self.fixed), _s(self.fixed)), style="bright_blue")
table.add_row(r"[?] {:>3} Test{} Ignored".format(len(self.ignored), _s(self.ignored)), style="grey58")
table.add_row(r"[!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)), style="yellow")
table.add_row(r"[✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)), style="red")
table.add_row(r"[bright blue][?] {:>3} Test{} Fixed".format(len(self.fixed), _s(self.fixed)))
table.add_row(r"[grey58][?] {:>3} Test{} Ignored".format(len(self.ignored), _s(self.ignored)))
table.add_row(r"[yellow][!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)))
table.add_row(r"[red][✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)))
console.print(table)

if len(self.could_fix):
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