Merge branch 'dev' of github.com:nf-core/tools into support-update-patch

CHANGELOG.md

@@ -40,6 +40,9 @@
 - Allow customization of the `nf-core` pipeline template when using `nf-core create` ([#1548](https://github.com/nf-core/tools/issues/1548))
 - Add Refgenie integration: updating of nextflow config files with a refgenie database ([#1090](https://github.com/nf-core/tools/pull/1090))
 - Fix `--key` option in `nf-core lint` when supplying a module lint test name ([#1681](https://github.com/nf-core/tools/issues/1681))
+- Add `no_git=True` when creating a new pipeline and initialising a git repository is not needed in `nf-core lint` and `nf-core bump-version` ([#1709](https://github.com/nf-core/tools/pull/1709))
+- Move `strip_ansi_code` function in lint to `utils.py`
+- Simplify control flow and don't use equality comparison for `None` and booleans
 
 ### Modules
 

docs/api/_src/api/lint.md

@@ -14,6 +14,6 @@ See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about
 ```{eval-rst}
 .. autoclass:: nf_core.lint.PipelineLint
     :members: _lint_pipeline
-    :private-members: _print_results, _get_results_md, _save_json_results, _wrap_quotes, _strip_ansi_codes
+    :private-members: _print_results, _get_results_md, _save_json_results, _wrap_quotes
     :show-inheritance:
 ```

nf_core/__main__.py

@@ -189,7 +189,7 @@ def launch(pipeline, id, revision, command_only, params_in, params_out, save_all
     launcher = nf_core.launch.Launch(
         pipeline, revision, command_only, params_in, params_out, save_all, show_hidden, url, id
     )
-    if launcher.launch_pipeline() == False:
+    if not launcher.launch_pipeline():
         sys.exit(1)
 
 

nf_core/launch.py

@@ -181,6 +181,7 @@ def launch_pipeline(self):
         # Build and launch the `nextflow run` command
         self.build_command()
         self.launch_workflow()
+        return True
 
     def get_pipeline_schema(self):
         """Load and validate the schema from the supplied pipeline"""

nf_core/lint/__init__.py

@@ -24,6 +24,7 @@
 from nf_core import __version__
 from nf_core.lint_utils import console
 from nf_core.utils import plural_s as _s
+from nf_core.utils import strip_ansi_codes
 
 log = logging.getLogger(__name__)
 
@@ -458,7 +459,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
-                        f"{self._strip_ansi_codes(msg, '`')}"
+                        f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.failed
                     ]
                 )
@@ -472,7 +473,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
-                        f"{self._strip_ansi_codes(msg, '`')}"
+                        f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.ignored
                     ]
                 )
@@ -486,7 +487,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
-                        f"{self._strip_ansi_codes(msg, '`')}"
+                        f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.fixed
                     ]
                 )
@@ -500,7 +501,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
-                        f"{self._strip_ansi_codes(msg, '`')}"
+                        f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.warned
                     ]
                 )
@@ -515,7 +516,7 @@ def _get_results_md(self):
                     [
                         (
                             f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html)"
-                            f" - {self._strip_ansi_codes(msg, '`')}"
+                            f" - {strip_ansi_codes(msg, '`')}"
                         )
                         for eid, msg in self.passed
                     ]
@@ -553,11 +554,11 @@ def _save_json_results(self, json_fn):
         results = {
             "nf_core_tools_version": nf_core.__version__,
             "date_run": now.strftime("%Y-%m-%d %H:%M:%S"),
-            "tests_pass": [[idx, self._strip_ansi_codes(msg)] for idx, msg in self.passed],
-            "tests_ignored": [[idx, self._strip_ansi_codes(msg)] for idx, msg in self.ignored],
-            "tests_fixed": [[idx, self._strip_ansi_codes(msg)] for idx, msg in self.fixed],
-            "tests_warned": [[idx, self._strip_ansi_codes(msg)] for idx, msg in self.warned],
-            "tests_failed": [[idx, self._strip_ansi_codes(msg)] for idx, msg in self.failed],
+            "tests_pass": [[idx, strip_ansi_codes(msg)] for idx, msg in self.passed],
+            "tests_ignored": [[idx, strip_ansi_codes(msg)] for idx, msg in self.ignored],
+            "tests_fixed": [[idx, strip_ansi_codes(msg)] for idx, msg in self.fixed],
+            "tests_warned": [[idx, strip_ansi_codes(msg)] for idx, msg in self.warned],
+            "tests_failed": [[idx, strip_ansi_codes(msg)] for idx, msg in self.failed],
             "num_tests_pass": len(self.passed),
             "num_tests_ignored": len(self.ignored),
             "num_tests_fixed": len(self.fixed),
@@ -590,11 +591,3 @@ def _wrap_quotes(self, files):
             files = [files]
         bfiles = [f"`{f}`" for f in files]
         return " or ".join(bfiles)
-
-    def _strip_ansi_codes(self, string, replace_with=""):
-        """Strip ANSI colouring codes from a string to return plain text.
-
-        Solution found on Stack Overflow: https://stackoverflow.com/a/14693789/713980
-        """
-        ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
-        return ansi_escape.sub(replace_with, string)

nf_core/lint/files_unchanged.py

@@ -133,7 +133,7 @@ def files_unchanged(self):
 
     test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")
     create_obj = nf_core.create.PipelineCreate(
-        None, None, None, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
+        None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
     )
     create_obj.init_pipeline()
 

nf_core/modules/info.py

@@ -45,9 +45,7 @@ def init_mod_name(self, module):
         Args:
             module: str: Module name to check
         """
-        if module is not None:
-            return module
-        else:
+        if module is None:
             local = questionary.confirm(
                 "Is the module locally installed?", style=nf_core.utils.nfcore_question_style
             ).unsafe_ask()
@@ -68,7 +66,8 @@ def init_mod_name(self, module):
                 module = questionary.autocomplete(
                     "Please select a new module", choices=modules, style=nf_core.utils.nfcore_question_style
                 ).unsafe_ask()
-            return module
+
+        return module
 
     def get_module_info(self):
         """Given the name of a module, parse meta.yml and print usage help."""
@@ -82,7 +81,7 @@ def get_module_info(self):
             self.meta = self.get_remote_yaml()
 
         # Could not find the meta
-        if self.meta == False:
+        if self.meta is False:
             raise UserWarning(f"Could not find module '{self.module}'")
 
         return self.generate_module_info_help()
@@ -113,7 +112,6 @@ def get_local_yaml(self):
                         return yaml.safe_load(fh)
 
             log.debug(f"Module '{self.module}' meta.yml not found locally")
-            return None
         else:
             module_base_path = os.path.join(self.dir, "modules")
             if self.module in os.listdir(module_base_path):
@@ -125,7 +123,8 @@ def get_local_yaml(self):
                         self.local_path = mod_dir
                         return yaml.safe_load(fh)
             log.debug(f"Module '{self.module}' meta.yml not found locally")
-            return None
+
+        return None
 
     def get_remote_yaml(self):
         """Attempt to get the meta.yml file from a remote repo.

nf_core/utils.py

@@ -65,14 +65,14 @@ def check_if_outdated(current_version=None, remote_version=None, source_url="htt
     if os.environ.get("NFCORE_NO_VERSION_CHECK", False):
         return True
     # Set and clean up the current version string
-    if current_version == None:
+    if current_version is None:
         current_version = nf_core.__version__
     current_version = re.sub(r"[^0-9\.]", "", current_version)
     # Build the URL to check against
     source_url = os.environ.get("NFCORE_VERSION_URL", source_url)
     source_url = f"{source_url}?v={current_version}"
     # Fetch and clean up the remote version
-    if remote_version == None:
+    if remote_version is None:
         response = requests.get(source_url, timeout=3)
         remote_version = re.sub(r"[^0-9\.]", "", response.text)
     # Check if we have an available update
@@ -993,3 +993,16 @@ def plural_es(list_or_int):
     """Return a 'es' if the input is not one or has not the length of one."""
     length = list_or_int if isinstance(list_or_int, int) else len(list_or_int)
     return "es" * (length != 1)
+
+
+# From Stack Overflow: https://stackoverflow.com/a/14693789/713980
+# Placed at top level as to only compile it once
+ANSI_ESCAPE_RE = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
+
+
+def strip_ansi_codes(string, replace_with=""):
+    """Strip ANSI colouring codes from a string to return plain text.
+
+    From Stack Overflow: https://stackoverflow.com/a/14693789/713980
+    """
+    return ANSI_ESCAPE_RE.sub(replace_with, string)

tests/test_bump_version.py

@@ -18,7 +18,7 @@ def test_bump_pipeline_version(datafiles, tmp_path):
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
     create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=test_pipeline_dir, plain=True
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
@@ -38,7 +38,7 @@ def test_dev_bump_pipeline_version(datafiles, tmp_path):
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
     create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=test_pipeline_dir, plain=True
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
@@ -57,7 +57,7 @@ def test_bump_nextflow_version(datafiles, tmp_path):
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
     create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=test_pipeline_dir, plain=True
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)

tests/test_download.py

@@ -105,7 +105,12 @@ def test_wf_use_local_configs(self, tmp_path):
         # Get a workflow and configs
         test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
         create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=test_pipeline_dir, plain=True
+            "testpipeline",
+            "This is a test pipeline",
+            "Test McTestFace",
+            no_git=True,
+            outdir=test_pipeline_dir,
+            plain=True,
         )
         create_obj.init_pipeline()
 

tests/test_lint.py

@@ -149,14 +149,6 @@ def test_wrap_quotes(self):
         md = self.lint_obj._wrap_quotes(["one", "two", "three"])
         assert md == "`one` or `two` or `three`"
 
-    def test_strip_ansi_codes(self):
-        """Check that we can make rich text strings plain
-
-        String prints ls examplefile.zip, where examplefile.zip is red bold text
-        """
-        stripped = self.lint_obj._strip_ansi_codes("ls \x1b[00m\x1b[01;31mexamplefile.zip\x1b[00m\x1b[01;31m")
-        assert stripped == "ls examplefile.zip"
-
     def test_sphinx_md_files(self):
         """Check that we have .md files for all lint module code,
         and that there are no unexpected files (eg. deleted lint tests)"""

tests/test_modules.py

@@ -44,7 +44,7 @@ def setUp(self):
         self.template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template")
         self.pipeline_dir = os.path.join(self.tmp_dir, "mypipeline")
         nf_core.create.PipelineCreate(
-            "mypipeline", "it is mine", "me", outdir=self.pipeline_dir, plain=True
+            "mypipeline", "it is mine", "me", no_git=True, outdir=self.pipeline_dir, plain=True
         ).init_pipeline()
         # Set up install objects
         print("Setting up install objects")

tests/test_utils.py

@@ -18,6 +18,15 @@
 from .utils import with_temporary_folder
 
 
+def test_strip_ansi_codes():
+    """Check that we can make rich text strings plain
+
+    String prints ls examplefile.zip, where examplefile.zip is red bold text
+    """
+    stripped = nf_core.utils.strip_ansi_codes("ls \x1b[00m\x1b[01;31mexamplefile.zip\x1b[00m\x1b[01;31m")
+    assert stripped == "ls examplefile.zip"
+
+
 class TestUtils(unittest.TestCase):
     """Class for utils tests"""
 
@@ -29,7 +38,12 @@ def setUp(self):
         self.tmp_dir = tempfile.mkdtemp()
         self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline")
         self.create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir, plain=True
+            "testpipeline",
+            "This is a test pipeline",
+            "Test McTestFace",
+            no_git=True,
+            outdir=self.test_pipeline_dir,
+            plain=True,
         )
         self.create_obj.init_pipeline()
         # Base Pipeline object on this directory