Merge branch 'dev' into stale-action

CHANGELOG.md

@@ -14,6 +14,10 @@
 
 ### Linting
 
+- Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
+- Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
+- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+
 ### Modules
 
 - Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
@@ -22,11 +26,13 @@
 
 - Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([#2177](https://github.com/nf-core/tools/pull/2177))
 - Fix `nf-core subworkflows test` not running subworkflow tests ([#2181](https://github.com/nf-core/tools/pull/2181))
+- Add tests for `nf-core subworkflows create-test-yml` ([#2219](https://github.com/nf-core/tools/pull/2219))
 
 ### General
 
 - `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
 - Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- update minimum version of rich to 13.3.1 ([#2185](https://github.com/nf-core/tools/pull/2185))
 - Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).

README.md

@@ -634,13 +634,13 @@ It's important to change the default value of a parameter in the `nextflow.confi
 The pipeline schema is linted as part of the main pipeline `nf-core lint` command,
 however sometimes it can be useful to quickly check the syntax of the JSONSchema without running a full lint run.
 
-Usage is `nf-core schema lint <schema>`, eg:
+Usage is `nf-core schema lint <schema>` (defaulting to `nextflow_schema.json`), eg:
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
 -->
 
-![`nf-core schema lint nextflow_schema.json`](docs/images/nf-core-schema-lint.svg)
+![`nf-core schema lint`](docs/images/nf-core-schema-lint.svg)
 
 ## Bumping a pipeline version number
 

nf_core/__main__.py

@@ -341,7 +341,7 @@ def lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, ma
     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/[/]
 
-    You can ignore tests using a file called [blue].nf-core-lint.yaml[/] [i](if you have a good reason!)[/].
+    You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/].
     See the documentation for details.
     """
 
@@ -1398,7 +1398,9 @@ def build(dir, no_prompts, web_only, url):
 
 # nf-core schema lint
 @schema.command()
-@click.argument("schema_path", type=click.Path(exists=True), required=True, metavar="<pipeline schema>")
+@click.argument(
+    "schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>"
+)
 def lint(schema_path):
     """
     Check that a given pipeline schema is valid.
@@ -1408,6 +1410,8 @@ def lint(schema_path):
 
     This function runs as part of the nf-core lint command, this is a convenience
     command that does just the schema linting nice and quickly.
+
+    If no schema path is provided, "nextflow_schema.json" will be used (if it exists).
     """
     schema_obj = nf_core.schema.PipelineSchema()
     try:

nf_core/components/components_command.py

@@ -6,6 +6,7 @@
 
 import yaml
 
+import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
 
@@ -162,24 +163,13 @@ def install_component_files(self, component_name, component_version, modules_rep
     def load_lint_config(self):
         """Parse a pipeline lint config file.
 
-        Look for a file called either `.nf-core-lint.yml` or
-        `.nf-core-lint.yaml` in the pipeline root directory and parse it.
-        (`.yml` takes precedence).
+        Load the '.nf-core.yml'  config file and extract
+        the lint config from it
 
         Add parsed config to the `self.lint_config` class attribute.
         """
-        config_fn = os.path.join(self.dir, ".nf-core-lint.yml")
-
-        # Pick up the file if it's .yaml instead of .yml
-        if not os.path.isfile(config_fn):
-            config_fn = os.path.join(self.dir, ".nf-core-lint.yaml")
-
-        # Load the YAML
-        try:
-            with open(config_fn, "r") as fh:
-                self.lint_config = yaml.safe_load(fh)
-        except FileNotFoundError:
-            log.debug(f"No lint config file found: {config_fn}")
+        _, tools_config = nf_core.utils.load_tools_config(self.dir)
+        self.lint_config = tools_config.get("lint", {})
 
     def check_modules_structure(self):
         """

nf_core/lint/nextflow_config.py

@@ -92,20 +92,22 @@ def nextflow_config(self):
     * Process-level configuration syntax still using the old Nextflow syntax, for example: ``process.$fastqc`` instead of ``process withName:'fastqc'``.
 
     .. tip:: You can choose to ignore tests for the presence or absence of specific config variables
-             by creating a file called ``.nf-core-lint.yml`` in the root of your pipeline and creating
+             by creating a file called ``.nf-core.yml`` in the root of your pipeline and creating
              a list the config variables that should be ignored. For example:
 
              .. code-block:: yaml
 
-                nextflow_config:
-                    - params.input
+                lint:
+                    nextflow_config:
+                        - params.input
 
              The other checks in this test (depreciated syntax etc) can not be individually identified,
              but you can skip the entire test block if you wish:
 
              .. code-block:: yaml
 
-                nextflow_config: False
+                lint:
+                    nextflow_config: False
     """
     passed = []
     warned = []

nf_core/modules/lint/main_nf.py

@@ -257,9 +257,26 @@ def check_process_section(self, lines, fix_version, progress_bar):
         self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
     for i, l in enumerate(lines):
         url = None
-        if _container_type(l) == "bioconda":
-            bioconda_packages = [b for b in l.split() if "bioconda::" in b]
         l = l.strip(" '\"")
+        if _container_type(l) == "conda":
+            bioconda_packages = [b for b in l.split() if "bioconda::" in b]
+            match = re.search(r"params\.enable_conda", l)
+            if match is None:
+                self.passed.append(
+                    (
+                        "deprecated_enable_conda",
+                        f"Deprecated parameter 'params.enable_conda' correctly not found in the conda definition",
+                        self.main_nf,
+                    )
+                )
+            else:
+                self.failed.append(
+                    (
+                        "deprecated_enable_conda",
+                        f"Found deprecated parameter 'params.enable_conda' in the conda definition",
+                        self.main_nf,
+                    )
+                )
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
@@ -471,7 +488,7 @@ def _fix_module_version(self, current_version, latest_version, singularity_tag,
     for line in lines:
         l = line.strip(" '\"")
         build_type = _container_type(l)
-        if build_type == "bioconda":
+        if build_type == "conda":
             new_lines.append(re.sub(rf"{current_version}", f"{latest_version}", line))
         elif build_type in ("singularity", "docker"):
             # Check that the new url is valid
@@ -516,8 +533,8 @@ def _get_build(response):
 
 def _container_type(line):
     """Returns the container type of a build."""
-    if re.search("bioconda::", line):
-        return "bioconda"
+    if line.startswith("conda"):
+        return "conda"
     if line.startswith("https://containers") or line.startswith("https://depot"):
         # Look for a http download URL.
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/3809435/713980

nf_core/subworkflow-template/tests/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { {{ subworkflow_name|upper }} } from '../../../../subworkflows/{{ org }}/{{ subworkflow_dir }}/main.nf'
 
-workflow test_{{ subworkflow_name }} {
+workflow test_{{ component_name_underscore }} {
     {% if has_meta %}
     input = [
         [ id:'test' ], // meta map

nf_core/subworkflows/test_yml_builder.py

@@ -139,7 +139,7 @@ def scrape_workflow_entry_points(self):
                 if match:
                     self.entry_points.append(match.group(1))
         if len(self.entry_points) == 0:
-            raise UserWarning("No workflow entry points found in 'self.module_test_main'")
+            raise UserWarning(f"No workflow entry points found in '{self.subworkflow_test_main}'")
 
     def build_all_tests(self):
         """
@@ -195,7 +195,7 @@ def build_single_test(self, entry_point):
                     ).strip()
                     ep_test["tags"] = [t.strip() for t in prompt_tags.split(",")]
 
-        ep_test["files"] = self.get_md5_sums(entry_point, ep_test["command"])
+        ep_test["files"] = self.get_md5_sums(ep_test["command"])
 
         return ep_test
 
@@ -272,7 +272,7 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
 
         return test_files
 
-    def get_md5_sums(self, entry_point, command, results_dir=None, results_dir_repeat=None):
+    def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
         """
         Recursively go through directories and subdirectories
         and generate tuples of (<file_path>, <md5sum>)

requirements.txt

@@ -15,6 +15,6 @@ questionary>=1.8.0
 refgenie
 requests
 requests_cache
-rich-click>=1.0.0
-rich>=10.7.0
+rich-click>=1.6.1
+rich>=13.3.1
 tabulate

tests/modules/create_test_yml.py

@@ -11,19 +11,19 @@
 @with_temporary_folder
 def test_modules_custom_yml_dumper(self, out_dir):
     """Try to create a yml file with the custom yml dumper"""
-    yml_output_path = os.path.join(out_dir, "test.yml")
+    yml_output_path = Path(out_dir, "test.yml")
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", self.pipeline_dir, False, "./", False, True)
     meta_builder.test_yml_output_path = yml_output_path
     meta_builder.tests = [{"testname": "myname"}]
     meta_builder.print_test_yml()
-    assert os.path.isfile(yml_output_path)
+    assert Path(yml_output_path).is_file()
 
 
 @with_temporary_folder
 def test_modules_test_file_dict(self, test_file_dir):
     """Create dict of test files and create md5 sums"""
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", self.pipeline_dir, False, "./", False, True)
-    with open(os.path.join(test_file_dir, "test_file.txt"), "w") as fh:
+    with open(Path(test_file_dir, "test_file.txt"), "w") as fh:
         fh.write("this line is just for testing")
     test_files = meta_builder.create_test_file_dict(test_file_dir)
     assert len(test_files) == 1
@@ -34,7 +34,7 @@ def test_modules_test_file_dict(self, test_file_dir):
 def test_modules_create_test_yml_get_md5(self, test_file_dir):
     """Get md5 sums from a dummy output"""
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", self.pipeline_dir, False, "./", False, True)
-    with open(os.path.join(test_file_dir, "test_file.txt"), "w") as fh:
+    with open(Path(test_file_dir, "test_file.txt"), "w") as fh:
         fh.write("this line is just for testing")
     test_files = meta_builder.get_md5_sums(command="dummy", results_dir=test_file_dir, results_dir_repeat=test_file_dir)
     assert test_files[0]["md5sum"] == "2191e06b28b5ba82378bcc0672d01786"
@@ -43,9 +43,7 @@ def test_modules_create_test_yml_get_md5(self, test_file_dir):
 def test_modules_create_test_yml_entry_points(self):
     """Test extracting test entry points from a main.nf file"""
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("bpipe/test", self.pipeline_dir, False, "./", False, True)
-    meta_builder.module_test_main = os.path.join(
-        self.nfcore_modules, "tests", "modules", "nf-core", "bpipe", "test", "main.nf"
-    )
+    meta_builder.module_test_main = Path(self.nfcore_modules, "tests", "modules", "nf-core", "bpipe", "test", "main.nf")
     meta_builder.scrape_workflow_entry_points()
     assert meta_builder.entry_points[0] == "test_bpipe_test"
 
@@ -55,7 +53,7 @@ def test_modules_create_test_yml_check_inputs(self):
     cwd = os.getcwd()
     os.chdir(self.nfcore_modules)
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("bpipe/test", ".", False, "./", False, True)
-    meta_builder.module_test_main = os.path.join(self.nfcore_modules, "tests", "modules", "bpipe", "test", "main.nf")
+    meta_builder.module_test_main = Path(self.nfcore_modules, "tests", "modules", "bpipe", "test", "main.nf")
     with pytest.raises(UserWarning) as excinfo:
         meta_builder.check_inputs()
     os.chdir(cwd)

tests/modules/lint.py

@@ -66,7 +66,7 @@ def test_modules_lint_gitlab_modules(self):
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
     module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 2
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
 
@@ -77,7 +77,7 @@ def test_modules_lint_multiple_remotes(self):
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
     module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 1
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
 
@@ -103,6 +103,6 @@ def test_modules_lint_patched_modules(self):
             all_modules=True,
         )
 
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 1
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0