Merge branch 'dev' into fix-1595

nf-core · May 25, 2022 · 5b76863 · 5b76863
2 parents 0126c04 + 67b2b48
commit 5b76863
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Showing 46 changed files with 419 additions and 484 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,10 @@
 
 - Fix bug in pipeline readme logo URL ([#1589](https://github.com/nf-core/tools/issues/1589))
 
+### Linting
+
+- Check that the `.prettierignore` file exists and that starts with the same content.
+
 ### General
 
 ### Modules

diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
@@ -14,7 +14,7 @@ def make_docs(docs_basedir, lint_tests, md_template):
             existing_docs.append(os.path.join(docs_basedir, fn))
 
     for test_name in lint_tests:
-        fn = os.path.join(docs_basedir, "{}.md".format(test_name))
+        fn = os.path.join(docs_basedir, f"{test_name}.md")
         if os.path.exists(fn):
             existing_docs.remove(fn)
         else:

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -65,10 +65,10 @@ def run_nf_core():
     rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1)
 
     # Print nf-core header
-    stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False)
+    stderr.print(f"\n[green]{' ' * 42},--.[grey39]/[green],-.", highlight=False)
     stderr.print("[blue]          ___     __   __   __   ___     [green]/,-._.--~\\", highlight=False)
-    stderr.print("[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
-    stderr.print("[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,", highlight=False)
+    stderr.print(r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {", highlight=False)
+    stderr.print(r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,", highlight=False)
     stderr.print("[green]                                          `._,._,'\n", highlight=False)
     stderr.print(
         f"[grey39]    nf-core/tools version {nf_core.__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
@@ -78,11 +78,11 @@ def run_nf_core():
         is_outdated, current_vers, remote_vers = nf_core.utils.check_if_outdated()
         if is_outdated:
             stderr.print(
-                "[bold bright_yellow]    There is a new version of nf-core/tools available! ({})".format(remote_vers),
+                f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
                 highlight=False,
             )
     except Exception as e:
-        log.debug("Could not check latest version: {}".format(e))
+        log.debug(f"Could not check latest version: {e}")
     stderr.print("\n")
 
     # Lanch the click cli
@@ -284,7 +284,7 @@ def create(name, description, author, version, no_git, force, outdir):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory [dim]\[default: current working directory][/]",
 )
 @click.option(
     "--release",
@@ -401,7 +401,7 @@ def remote(ctx, keywords, json):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: Current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
 def local(ctx, keywords, json, dir):
     """
@@ -425,7 +425,7 @@ def local(ctx, keywords, json, dir):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-f", "--force", is_flag=True, default=False, help="Force reinstallation of module if it already exists")
@@ -456,7 +456,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("-f", "--force", is_flag=True, default=False, help="Force update of module")
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
@@ -505,7 +505,7 @@ def update(ctx, tool, dir, force, prompt, sha, all, preview, save_diff):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 def remove(ctx, dir, tool):
     """
@@ -627,7 +627,7 @@ def lint(ctx, tool, dir, key, all, local, passed):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: Current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
 def info(ctx, tool, dir):
     """
@@ -784,7 +784,7 @@ def validate(pipeline, params):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("--no-prompts", is_flag=True, help="Do not confirm changes, just update parameters and exit")
 @click.option("--web-only", is_flag=True, help="Skip building using Nextflow config, just launch the web tool")
@@ -886,7 +886,7 @@ def docs(schema_path, output, format, force, columns):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option(
     "-n", "--nextflow", is_flag=True, default=False, help="Bump required nextflow version instead of pipeline version"
@@ -929,7 +929,7 @@ def bump_version(new_version, dir, nextflow):
     "--dir",
     type=click.Path(exists=True),
     default=".",
-    help="Pipeline directory. [dim]\[default: current working directory][/]",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("-b", "--from-branch", type=str, help="The git branch to use to fetch workflow variables.")
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")

diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
@@ -31,16 +31,16 @@ def bump_pipeline_version(pipeline_obj, new_version):
     if not current_version:
         raise UserWarning("Could not find config variable 'manifest.version'")
 
-    log.info("Changing version number from '{}' to '{}'".format(current_version, new_version))
+    log.info(f"Changing version number from '{current_version}' to '{new_version}'")
 
     # nextflow.config - workflow manifest version
     update_file_version(
         "nextflow.config",
         pipeline_obj,
         [
             (
-                r"version\s*=\s*[\'\"]?{}[\'\"]?".format(current_version.replace(".", r"\.")),
-                "version = '{}'".format(new_version),
+                rf"version\s*=\s*[\'\"]?{re.escape(current_version)}[\'\"]?",
+                f"version = '{new_version}'",
             )
         ],
     )
@@ -61,16 +61,16 @@ def bump_nextflow_version(pipeline_obj, new_version):
     new_version = re.sub(r"^[^0-9\.]*", "", new_version)
     if not current_version:
         raise UserWarning("Could not find config variable 'manifest.nextflowVersion'")
-    log.info("Changing Nextlow version number from '{}' to '{}'".format(current_version, new_version))
+    log.info(f"Changing Nextlow version number from '{current_version}' to '{new_version}'")
 
     # nextflow.config - manifest minimum nextflowVersion
     update_file_version(
         "nextflow.config",
         pipeline_obj,
         [
             (
-                r"nextflowVersion\s*=\s*[\'\"]?!>={}[\'\"]?".format(current_version.replace(".", r"\.")),
-                "nextflowVersion = '!>={}'".format(new_version),
+                rf"nextflowVersion\s*=\s*[\'\"]?!>={re.escape(current_version)}[\'\"]?",
+                f"nextflowVersion = '!>={new_version}'",
             )
         ],
     )
@@ -82,8 +82,8 @@ def bump_nextflow_version(pipeline_obj, new_version):
         [
             (
                 # example: - NXF_VER: '20.04.0'
-                r"- NXF_VER: [\'\"]{}[\'\"]".format(current_version.replace(".", r"\.")),
-                "- NXF_VER: '{}'".format(new_version),
+                rf"- NXF_VER: [\'\"]{re.escape(current_version)}[\'\"]",
+                f"- NXF_VER: '{new_version}'",
             )
         ],
     )
@@ -94,17 +94,13 @@ def bump_nextflow_version(pipeline_obj, new_version):
         pipeline_obj,
         [
             (
-                r"nextflow%20DSL2-%E2%89%A5{}-23aa62.svg".format(current_version.replace(".", r"\.")),
-                "nextflow%20DSL2-%E2%89%A5{}-23aa62.svg".format(new_version),
+                rf"nextflow%20DSL2-%E2%89%A5{re.escape(current_version)}-23aa62.svg",
+                f"nextflow%20DSL2-%E2%89%A5{new_version}-23aa62.svg",
             ),
             (
                 # example: 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=20.04.0`)
-                r"1\.\s*Install\s*\[`Nextflow`\]\(https:\/\/www\.nextflow\.io\/docs\/latest\/getstarted\.html#installation\)\s*\(`>={}`\)".format(
-                    current_version.replace(".", r"\.")
-                ),
-                "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>={}`)".format(
-                    new_version
-                ),
+                rf"1\.\s*Install\s*\[`Nextflow`\]\(https:\/\/www\.nextflow\.io\/docs\/latest\/getstarted\.html#installation\)\s*\(`>={re.escape(current_version)}`\)",
+                f"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>={new_version}`)",
             ),
         ],
     )
@@ -130,7 +126,7 @@ def update_file_version(filename, pipeline_obj, patterns):
         with open(fn, "r") as fh:
             content = fh.read()
     except FileNotFoundError:
-        log.warning("File not found: '{}'".format(fn))
+        log.warning(f"File not found: '{fn}'")
         return
 
     replacements = []
@@ -142,7 +138,7 @@ def update_file_version(filename, pipeline_obj, patterns):
         for line in content.splitlines():
 
             # Match the pattern
-            matches_pattern = re.findall("^.*{}.*$".format(pattern[0]), line)
+            matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
             if matches_pattern:
                 found_match = True
 
@@ -160,12 +156,12 @@ def update_file_version(filename, pipeline_obj, patterns):
         if found_match:
             content = "\n".join(newcontent) + "\n"
         else:
-            log.error("Could not find version number in {}: '{}'".format(filename, pattern))
+            log.error(f"Could not find version number in {filename}: '{pattern}'")
 
-    log.info("Updated version in '{}'".format(filename))
+    log.info(f"Updated version in '{filename}'")
     for replacement in replacements:
-        stderr.print("          [red] - {}".format(replacement[0].strip()), highlight=False)
-        stderr.print("          [green] + {}".format(replacement[1].strip()), highlight=False)
+        stderr.print(f"          [red] - {replacement[0].strip()}", highlight=False)
+        stderr.print(f"          [green] + {replacement[1].strip()}", highlight=False)
     stderr.print("\n")
 
     with open(fn, "w") as fh:

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -186,7 +186,7 @@ def download_pipeline_logo(self, url, img_fn):
             except (ConnectionError, UserWarning) as e:
                 # Something went wrong - try again
                 log.warning(e)
-                log.error(f"Connection error - retrying")
+                log.error("Connection error - retrying")
                 continue
 
             # Write the new logo to the file