[Feature] Flexible linting for actionsci and multiqc_config

.github/CONTRIBUTING.md

@@ -75,7 +75,7 @@ New features should also come with new tests, to keep the test-coverage high (we
 You can try running the tests locally before pushing code using the following command:
 
 ```bash
-pytest --color=yes tests/
+pytest --color=yes
 ```
 
 ### Lint Tests

docs/api/_src/pipeline_lint_tests/multiqc_config.md

@@ -0,0 +1,4 @@
+multiqc_config
+===============
+
+.. automethod:: nf_core.lint.PipelineLint.multiqc_config

nf_core/__init__.py

@@ -4,6 +4,4 @@
 Shouldn't do much, as everything is under subcommands.
 """
 
-import pkg_resources
-
-__version__ = pkg_resources.get_distribution("nf_core").version
+from .version import __version__

nf_core/lint/__init__.py

@@ -153,6 +153,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .files_unchanged import files_unchanged
     from .merge_markers import merge_markers
     from .modules_json import modules_json
+    from .multiqc_config import multiqc_config
     from .nextflow_config import nextflow_config
     from .pipeline_name_conventions import pipeline_name_conventions
     from .pipeline_todos import pipeline_todos
@@ -205,6 +206,7 @@ def _get_all_lint_tests(release_mode):
             "actions_schema_validation",
             "merge_markers",
             "modules_json",
+            "multiqc_config",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self):

nf_core/lint/actions_ci.py

@@ -85,9 +85,15 @@ def actions_ci(self):
 
     # Check that the action is turned on for the correct events
     try:
-        expected = {"push": {"branches": ["dev"]}, "pull_request": None, "release": {"types": ["published"]}}
         # NB: YAML dict key 'on' is evaluated to a Python dict key True
-        assert ciwf[True] == expected
+        assert "dev" in ciwf[True]["push"]["branches"]
+        pr_subtree = ciwf[True]["pull_request"]
+        assert (
+            pr_subtree == None
+            or ("branches" in pr_subtree and "dev" in pr_subtree["branches"])
+            or ("ignore_branches" in pr_subtree and not "dev" in pr_subtree["ignore_branches"])
+        )
+        assert "published" in ciwf[True]["release"]["types"]
     except (AssertionError, KeyError, TypeError):
         failed.append("'.github/workflows/ci.yml' is not triggered on expected events")
     else:

nf_core/lint/files_unchanged.py

@@ -45,7 +45,6 @@ def files_unchanged(self):
     Files that can have additional content but must include the template contents::
 
         .gitignore
-        assets/multiqc_config.yaml
 
     .. 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 linting config file. For example:
@@ -54,7 +53,6 @@ def files_unchanged(self):
 
                 files_unchanged:
                   - .github/workflows/branch.yml
-                  - assets/multiqc_config.yaml
 
     """
 
@@ -102,7 +100,6 @@ def files_unchanged(self):
     ]
     files_partial = [
         [".gitignore", "foo"],
-        [os.path.join("assets", "multiqc_config.yaml")],
     ]
 
     # Only show error messages from pipeline creation

nf_core/lint/multiqc_config.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+import os
+import yaml
+
+
+def multiqc_config(self):
+    """Make sure basic multiQC plugins are installed and plots are exported
+    Basic template:
+    report_comment: >
+        This report has been generated by the <a href="https://github.com/nf-core/quantms" target="_blank">nf-core/quantms</a>
+        analysis pipeline. For information about how to interpret these results, please see the
+        <a href="https://nf-co.re/quantms" target="_blank">documentation</a>.
+    report_section_order:
+        software_versions:
+            order: -1000
+        nf-core-quantms-summary:
+            order: -1001
+
+    export_plots: true
+    """
+    passed = []
+    failed = []
+
+    fn = os.path.join(self.wf_path, "assets", "multiqc_config.yaml")
+
+    # Return a failed status if we can't find the file
+    if not os.path.isfile(fn):
+        return {"failed": ["'assets/multiqc_config.yaml' not found"]}
+
+    try:
+        with open(fn, "r") as fh:
+            mqc_yml = yaml.safe_load(fh)
+    except Exception as e:
+        return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
+
+    # Check that the report_comment exists and matches
+    try:
+        assert "report_section_order" in mqc_yml
+        orders = dict()
+        summary_plugin_name = "nf-core-" + self.pipeline_name + "-summary"
+        min_plugins = ["software_versions", summary_plugin_name]
+        for plugin in min_plugins:
+            assert plugin in mqc_yml["report_section_order"]
+            assert "order" in mqc_yml["report_section_order"][plugin]
+            plugin_order = mqc_yml["report_section_order"][plugin]["order"]
+            assert plugin_order < 0
+
+        for plugin in mqc_yml["report_section_order"]:
+            if "order" in mqc_yml["report_section_order"][plugin]:
+                orders[plugin] = mqc_yml["report_section_order"][plugin]["order"]
+
+        assert orders[summary_plugin_name] == min(orders.values())
+        orders.pop(summary_plugin_name)
+        assert orders["software_versions"] == min(orders.values())
+    except (AssertionError, KeyError, TypeError):
+        failed.append(
+            "'assets/multiqc_config.yaml' does not follow the ordering scheme of the minimally required plugins."
+        )
+    else:
+        passed.append("'assets/multiqc_config.yaml' follows the ordering scheme of the minimally required plugins.")
+
+    # Check that the minimum plugins exist and are coming first in the summary
+    try:
+        assert "report_comment" in mqc_yml
+        assert (
+            mqc_yml["report_comment"].strip()
+            == 'This report has been generated by the <a href="https://github.com/nf-core/%s" target="_blank">nf-core/%s</a> '
+            "analysis pipeline. For information about how to interpret these results, please see the "
+            '<a href="https://nf-co.re/%s" target="_blank">documentation</a>.'
+            % (
+                self.pipeline_name,
+                self.pipeline_name,
+                self.pipeline_name,
+            )
+        )
+    except (AssertionError, KeyError, TypeError):
+        failed.append("'assets/multiqc_config.yaml' does not contain a matching report_comment.")
+    else:
+        passed.append("'assets/multiqc_config.yaml' contains a matching report_comment.")
+
+    # Check that export_plots is activated
+    try:
+        assert "export_plots" in mqc_yml
+        assert mqc_yml["export_plots"] == True
+    except (AssertionError, KeyError, TypeError):
+        failed.append("'assets/multiqc_config.yaml' does not contain 'export_plots: true'.")
+    else:
+        passed.append("'assets/multiqc_config.yaml' contains 'export_plots: true'.")
+
+    return {"passed": passed, "failed": failed}

nf_core/version.py

@@ -0,0 +1 @@
+__version__ = "2.4dev"

pytest.ini

@@ -1,3 +1,5 @@
 [pytest]
 filterwarnings =
     ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140
+testpaths =
+    tests

setup.py

@@ -2,7 +2,13 @@
 
 from setuptools import setup, find_packages
 
-version = "2.4dev"
+versionfile = "nf_core/version.py"
+try:
+    execfile(versionfile)
+except:
+    exec(open(versionfile).read())
+
+version = __version__
 
 with open("README.md") as f:
     readme = f.read()