Merge branch 'dev' into update-module

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Add `CITATION.cff` [#361](https://github.com/nf-core/tools/issues/361)
 - Add Gitpod and Mamba profiles to the pipeline template ([#1673](https://github.com/nf-core/tools/pull/1673))
 - Remove call to `getGenomeAttribute` in `main.nf` when running `nf-core create` without iGenomes ([#1670](https://github.com/nf-core/tools/issues/1670))
+- Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
 
 ### Linting
 
@@ -39,6 +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
 
@@ -53,6 +57,11 @@
 - Fix inconsistencies in the `--save-diff` flag `nf-core modules update`. Refactor `nf-core modules update` ([#1536](https://github.com/nf-core/tools/pull/1536))
 - Fix bug in `ModulesJson.check_up_to_date` causing it to ask for the remote of local modules
 - Handle errors when updating module version with `nf-core modules update --fix-version` ([#1671](https://github.com/nf-core/tools/pull/1671))
+- Make `nf-core modules update --save-diff` work when files were created or removed ([#1694](https://github.com/nf-core/tools/issues/1694))
+- Get the latest common build for Docker and Singularity containers of a module ([#1702](https://github.com/nf-core/tools/pull/1702))
+- Add short option for `--no-pull` option in `nf-core modules`
+- Add `nf-core modules patch` command ([#1312](https://github.com/nf-core/tools/issues/1312))
+- Add support for patch in `nf-core modules update` command ([#1312](https://github.com/nf-core/tools/issues/1312))
 
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 

README.md

@@ -1176,6 +1176,49 @@ INFO     Removing star/align
 
 You can pass the module name as an optional argument to `nf-core modules remove` instead of using the cli prompt, eg: `nf-core modules remove fastqc`. To specify the pipeline directory, use `--dir <pipeline_dir>`.
 
+### Create a patch file for minor local changes in a module
+
+If you want to make a minor change to a module but still keep it up date with the remote version, you can create a patch file using `nf-core modules patch`.
+
+```console
+$ nf-core modules patch
+
+                                          ,--./,-.
+          ___     __   __   __   ___     /,-._.--~\
+    |\ | |__  __ /  ` /  \ |__) |__         }  {
+    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
+                                          `._,._,'
+
+    nf-core/tools version 2.5.dev0 - https://nf-co.re
+
+
+? Tool: bismark/align
+INFO     Changes in module 'nf-core/modules/bismark/align'
+INFO     Changes in 'bismark/align/main.nf':
+
+ --- modules/nf-core/modules/bismark/align/main.nf
+ +++ modules/nf-core/modules/bismark/align/main.nf
+ @@ -19,8 +19,7 @@
+      }
+
+      input:
+ -    tuple val(meta), path(reads)
+ -    path index
+ +    tuple val(meta), path(reads), path index
+
+      output:
+      tuple val(meta), path("*bam")       , emit: bam
+
+
+INFO     'modules/nf-core/modules/bismark/align/functions.nf' is unchanged
+INFO     'modules/nf-core/modules/bismark/align/meta.yml' is unchanged
+INFO     Patch file of 'nf-core/modules/bismark/align' written to 'modules/nf-core/modules/bismark/align/bismark-align.diff'
+```
+
+The generated patches work with `nf-core modules update`: when you install a new version of the module, the command tries to apply
+the patch automatically. The patch application fails if the new version of the module modifies the same lines as the patch. In this case,
+the patch new version is installed but the old patch file is preversed.
+
 ### Create a new module
 
 This command creates a new nf-core module from the nf-core module template.

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

@@ -2,9 +2,7 @@
 """ nf-core: Helper tools for use with nf-core Nextflow pipelines. """
 import logging
 import os
-import re
 import sys
-from email.policy import default
 
 import rich.console
 import rich.logging
@@ -49,7 +47,7 @@
     "nf-core modules": [
         {
             "name": "For pipelines",
-            "commands": ["list", "info", "install", "update", "remove"],
+            "commands": ["list", "info", "install", "update", "remove", "patch"],
         },
         {
             "name": "Developing new modules",
@@ -191,7 +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)
 
 
@@ -350,6 +348,7 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdow
 )
 @click.option("-b", "--branch", type=str, default=None, help="Branch of git repository hosting modules.")
 @click.option(
+    "-N",
     "--no-pull",
     is_flag=True,
     default=False,
@@ -539,6 +538,38 @@ def update(ctx, tool, dir, force, prompt, sha, all, preview, save_diff):
         sys.exit(1)
 
 
+# nf-core modules patch
+@modules.command()
+@click.pass_context
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option(
+    "-d",
+    "--dir",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
+def patch(ctx, tool, dir):
+    """
+    Create a patch file for minor changes in a module
+
+    Checks if a module has been modified locally and creates a patch file
+    describing how the module has changed from the remote version
+    """
+    try:
+        module_patch = nf_core.modules.ModulePatch(
+            dir,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+            ctx.obj["modules_repo_base_path"],
+        )
+        module_patch.patch(tool)
+    except (UserWarning, LookupError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core modules remove
 @modules.command()
 @click.pass_context

nf_core/bump_version.py

@@ -6,7 +6,6 @@
 import logging
 import os
 import re
-import sys
 
 import rich.console
 

nf_core/create.py

@@ -2,6 +2,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+import configparser
 import imghdr
 import logging
 import os
@@ -490,7 +491,24 @@ def download_pipeline_logo(self, url, img_fn):
             break
 
     def git_init_pipeline(self):
-        """Initialises the new pipeline as a Git repository and submits first commit."""
+        """Initialises the new pipeline as a Git repository and submits first commit.
+
+        Raises:
+            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
+        """
+        # Check that the default branch is not dev
+        try:
+            default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
+        except configparser.Error:
+            default_branch = None
+            log.debug("Could not read init.defaultBranch")
+        if default_branch == "dev" or default_branch == "TEMPLATE":
+            raise UserWarning(
+                f"Your Git defaultBranch is set to '{default_branch}', which is incompatible with nf-core.\n"
+                "This can be modified with the command [white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
+                "Pipeline git repository is not initialised."
+            )
+        # Initialise pipeline
         log.info("Initialising pipeline git repository")
         repo = git.Repo.init(self.outdir)
         repo.git.add(A=True)

nf_core/launch.py

@@ -12,7 +12,6 @@
 import webbrowser
 
 import questionary
-import requests
 from rich.console import Console
 from rich.markdown import Markdown
 from rich.prompt import Confirm
@@ -182,6 +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/licences.py

@@ -6,7 +6,6 @@
 import json
 import logging
 import os
-import re
 
 import requests
 import rich.console

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/actions_schema_validation.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import glob
-import json
 import logging
 import os
 

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/lint/modules_json.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from logging import warn
-
 from nf_core.modules.modules_command import ModuleCommand
 from nf_core.modules.modules_json import ModulesJson
 

nf_core/lint/schema_description.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from logging import warn
-
 import nf_core.schema
 
 

nf_core/lint/schema_lint.py

@@ -2,8 +2,6 @@
 
 import logging
 
-import jsonschema
-
 import nf_core.schema
 
 

nf_core/modules/__init__.py

@@ -9,6 +9,7 @@
 from .modules_json import ModulesJson
 from .modules_repo import ModulesRepo
 from .mulled import MulledImageNameGenerator
+from .patch import ModulePatch
 from .remove import ModuleRemove
 from .test_yml_builder import ModulesTestYmlBuilder
 from .update import ModuleUpdate

nf_core/modules/bump_versions.py

@@ -7,7 +7,6 @@
 from __future__ import print_function
 
 import logging
-import os
 import re
 
 import questionary