Merge branch 'dev' into empty-file-stub

.github/workflows/pytest.yml

@@ -39,16 +39,6 @@ jobs:
         id: conditions
         run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
 
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-        if: ${{ env.run-tests == 'true' }}
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-        if: ${{ env.run-tests == 'true' }}
     outputs:
       python-version: ${{ matrix.python-version }}
       runner: ${{ matrix.runner }}
@@ -97,7 +87,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'

.gitpod.yml

@@ -6,6 +6,9 @@ tasks:
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
       nextflow self-update
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))
 - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
 - Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
 ### Download
 
@@ -42,6 +43,7 @@
 - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)).
 - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)).
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 

nf_core/components/install.py

@@ -127,6 +127,8 @@ def install(self, component, silent=False):
             self.install_included_components(component_dir)
 
         if not silent:
+            modules_json.load()
+            modules_json.dump(run_prettier=True)
             # Print include statement
             component_name = "_".join(component.upper().split("/"))
             log.info(f"Use the following statement to include this {self.component_type[:-1]}:")

nf_core/components/update.py

@@ -288,20 +288,21 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 updated.append(component)
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
-                if not silent and not self.update_all and len(modules_to_update + subworkflows_to_update) > 0:
-                    log.warning(
-                        f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
-                        "It is advised to keep all your modules and subworkflows up to date.\n"
-                        "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
-                    )
-                    if self.update_deps:
-                        recursive_update = True
-                    else:
-                        recursive_update = questionary.confirm(
-                            "Would you like to continue updating all modules and subworkflows?",
-                            default=True,
-                            style=nf_core.utils.nfcore_question_style,
-                        ).unsafe_ask()
+                if not silent and len(modules_to_update + subworkflows_to_update) > 0:
+                    if not self.update_all:
+                        log.warning(
+                            f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
+                            "It is advised to keep all your modules and subworkflows up to date.\n"
+                            "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
+                        )
+                        if self.update_deps:
+                            recursive_update = True
+                        else:
+                            recursive_update = questionary.confirm(
+                                "Would you like to continue updating all modules and subworkflows?",
+                                default=True,
+                                style=nf_core.utils.nfcore_question_style,
+                            ).unsafe_ask()
                 if recursive_update and len(modules_to_update + subworkflows_to_update) > 0:
                     # Update linked components
                     self.update_linked_components(modules_to_update, subworkflows_to_update, updated)
@@ -323,8 +324,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 )
         elif not all_patches_successful and not silent:
             log.info(f"Updates complete. Please apply failed patch{plural_es(components_info)} manually.")
+            self.modules_json.load()
+            self.modules_json.dump(run_prettier=True)
         elif not silent:
             log.info("Updates complete :sparkles:")
+            self.modules_json.load()
+            self.modules_json.dump(run_prettier=True)
 
         return exit_value
 

nf_core/modules/modules_json.py

@@ -6,6 +6,7 @@
 import shutil
 import tempfile
 from pathlib import Path
+from typing import Union
 
 import git
 import questionary
@@ -41,7 +42,7 @@ def __init__(self, pipeline_dir):
         self.modules_dir = Path(self.dir, "modules")
         self.subworkflows_dir = Path(self.dir, "subworkflows")
         self.modules_json_path = Path(self.dir, "modules.json")
-        self.modules_json = None
+        self.modules_json: Union(dict, None) = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
         self.pipeline_components = None
@@ -1035,13 +1036,17 @@ def get_component_branch(self, component_type, component, repo_url, install_dir)
             )
         return branch
 
-    def dump(self):
+    def dump(self, run_prettier: bool = False):
         """
         Sort the modules.json, and write it to file
         """
         # Sort the modules.json
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        dump_json_with_prettier(self.modules_json_path, self.modules_json)
+        if run_prettier:
+            dump_json_with_prettier(self.modules_json_path, self.modules_json)
+        else:
+            with open(self.modules_json_path, "w") as fh:
+                json.dump(self.modules_json, fh, indent=4)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [

nf_core/pipeline-template/.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files