Merge pull request #1793 from nf-core/dev

Dev -> Master v2.5.1

.github/RELEASE_CHECKLIST.md

@@ -2,16 +2,17 @@
 
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
-3. Check whether the GitHub Actions workflow scripts need updating of the Nextflow versions
+3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
 5. Make sure all CI tests are passing!
 6. Create a PR from `dev` to `master`
 7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
 8. Request review (2 approvals required)
 9. Merge the PR into `master`
-10. Wait for CI tests on the commit to passed
-11. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
-12. Create a new release copying the `CHANGELOG` for that release into the description section.
+10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
+11. Wait for CI tests on the commit to passed
+12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+13. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 

.github/workflows/deploy-pypi.yml

@@ -31,6 +31,6 @@ jobs:
 
       - name: Publish dist to PyPI
         if: github.repository == 'nf-core/tools'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.pypi_password }}

CHANGELOG.md

@@ -1,5 +1,12 @@
 # nf-core/tools: Changelog
 
+## [v2.5.1 - Gold Otter Patch](https://github.com/nf-core/tools/releases/tag/2.5.1) - [2022-08-31]
+
+- Patch release to fix black linting in pipelines ([#1789](https://github.com/nf-core/tools/pull/1789))
+- Add isort options to pyproject.toml ([#1792](https://github.com/nf-core/tools/pull/1792))
+- Lint pyproject.toml file exists and content ([#1795](https://github.com/nf-core/tools/pull/1795))
+- Update GitHub PyPI package release action to v1 ([#1785](https://github.com/nf-core/tools/pull/1785))
+
 ## [v2.5 - Gold Otter](https://github.com/nf-core/tools/releases/tag/2.5) - [2022-08-30]
 
 ### Template

CITATION.cff

@@ -13,8 +13,8 @@ authors:
     given-names: Johannes
   - family-names: Wilm
     given-names: Andreas
-  - family-names: Ulysse Garcia
-    given-names: Maxime
+  - family-names: Garcia
+    given-names: Maxime Ulysse
   - family-names: Di Tommaso
     given-names: Paolo
   - family-names: Nahnsen
@@ -39,8 +39,8 @@ prefered-citation:
       given-names: Johannes
     - family-names: Wilm
       given-names: Andreas
-    - family-names: Ulysse Garcia
-      given-names: Maxime
+    - family-names: Garcia
+      given-names: Maxime Ulysse
     - family-names: Di Tommaso
       given-names: Paolo
     - family-names: Nahnsen

nf_core/lint/files_exist.py

@@ -73,6 +73,7 @@ def files_exist(self):
         .github/workflows/awstest.yml
         .github/workflows/awsfulltest.yml
         lib/WorkflowPIPELINE.groovy
+        pyproject.toml
 
     Files that *must not* be present:
 
@@ -174,6 +175,7 @@ def files_exist(self):
         [os.path.join(".github", "workflows", "awsfulltest.yml")],
         [os.path.join("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy")],
         ["modules.json"],
+        ["pyproject.toml"],
     ]
 
     # List of strings. Fails / warns if any of the strings exist.

nf_core/lint/files_unchanged.py

@@ -50,6 +50,7 @@ def files_unchanged(self):
 
         .gitignore
         .prettierignore
+        pyproject.toml
 
     .. tip:: You can configure the ``nf-core lint`` tests to ignore any of these checks by setting
              the ``files_unchanged`` key as follows in your ``.nf-core.yml`` config file. For example:
@@ -110,7 +111,7 @@ def files_unchanged(self):
         [os.path.join("lib", "NfcoreTemplate.groovy")],
     ]
     files_partial = [
-        [".gitignore", ".prettierignore"],
+        [".gitignore", ".prettierignore", "pyproject.toml"],
     ]
 
     # Only show error messages from pipeline creation

nf_core/pipeline-template/bin/check_samplesheet.py

@@ -98,7 +98,9 @@ def _validate_pair(self, row):
         """Assert that read pairs have the same file extension. Report pair status."""
         if row[self._first_col] and row[self._second_col]:
             row[self._single_col] = False
-            if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]:
+            first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
+            second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
+            if first_col_suffix != second_col_suffix:
                 raise AssertionError("FASTQ pairs must have the same file extensions.")
         else:
             row[self._single_col] = True
@@ -157,7 +159,7 @@ def sniff_format(handle):
     handle.seek(0)
     sniffer = csv.Sniffer()
     if not sniffer.has_header(peek):
-        logger.critical(f"The given sample sheet does not appear to contain a header.")
+        logger.critical("The given sample sheet does not appear to contain a header.")
         sys.exit(1)
     dialect = sniffer.sniff(peek)
     return dialect
@@ -195,7 +197,8 @@ def check_samplesheet(file_in, file_out):
         reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
         # Validate the existence of the expected header columns.
         if not required_columns.issubset(reader.fieldnames):
-            logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.")
+            req_cols = ", ".join(required_columns)
+            logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
             sys.exit(1)
         # Validate each row.
         checker = RowChecker()

nf_core/pipeline-template/pyproject.toml

@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.5"
+version = "2.5.1"
 
 with open("README.md") as f:
     readme = f.read()