Migrate component create to nf test

.github/workflows/lint-code.yml

@@ -92,8 +92,29 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
-      - run: pip install mypy types-PyYAML
+          python-version: 3.11
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
       - name: Get Python changed files
         id: changed-py-files
         uses: tj-actions/changed-files@v23

.github/workflows/pytest.yml

@@ -64,6 +64,21 @@ jobs:
         with:
           version: "latest-everything"
 
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
       - name: Test with pytest
         run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
 

.prettierignore

@@ -4,4 +4,5 @@ slackreport.json
 docs/api/_build
 testing
 nf_core/module-template/modules/meta.yml
-nf_core/module-template/tests/test.yml
+nf_core/module-template/modules/tests/tags.yml
+nf_core/subworkflow-template/subworkflows/tests/tags.yml

Dockerfile

@@ -31,6 +31,11 @@ ENV NXF_VER ${NXF_VER}
 RUN curl -s https://get.nextflow.io | bash \
     && mv nextflow /usr/local/bin \
     && chmod a+rx /usr/local/bin/nextflow
+# Install nf-test
+RUN curl -fsSL https://code.askimed.com/install/nf-test | bash \
+    && mv nf-test /usr/local/bin \
+    && chmod a+rx /usr/local/bin/nf-test
+
 # Add the nf-core source files to the image
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core

nf_core/__main__.py

@@ -652,7 +652,7 @@ def install(ctx, tool, dir, prompt, force, sha):
             ctx.obj["modules_repo_no_pull"],
         )
         exit_status = module_install.install(tool)
-        if not exit_status and all:
+        if not exit_status:
             sys.exit(1)
     except (UserWarning, LookupError) as e:
         log.error(e)
@@ -673,7 +673,9 @@ def install(ctx, tool, dir, prompt, force, sha):
 @click.option("-f", "--force", is_flag=True, default=False, help="Force update of module")
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-@click.option("-a", "--all", is_flag=True, default=False, help="Update all modules installed in pipeline")
+@click.option(
+    "-a", "--all", "install_all", is_flag=True, default=False, help="Update all modules installed in pipeline"
+)
 @click.option(
     "-x/-y",
     "--preview/--no-preview",
@@ -696,7 +698,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, tool, dir, force, prompt, sha, all, preview, save_diff, update_deps):
+def update(ctx, tool, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 modules within a pipeline.
 
@@ -719,7 +721,7 @@ def update(ctx, tool, dir, force, prompt, sha, all, preview, save_diff, update_d
             ctx.obj["modules_repo_no_pull"],
         )
         exit_status = module_install.update(tool)
-        if not exit_status and all:
+        if not exit_status and install_all:
             sys.exit(1)
     except (UserWarning, LookupError) as e:
         log.error(e)
@@ -849,34 +851,35 @@ def create_module(
         sys.exit(1)
 
 
-# nf-core modules create-test-yml
-@modules.command("create-test-yml")
+# nf-core modules create-snapshot
+@modules.command("create-snapshot")
 @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=".", metavar="<nf-core/modules directory>")
 @click.option("-t", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
-@click.option("-o", "--output", type=str, help="Path for output YAML file")
-@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output YAML file if it already exists")
 @click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
-def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
+@click.option("-u", "--update", is_flag=True, default=False, help="Update existing snapshots")
+def create_snapshot(ctx, tool, dir, run_tests, no_prompts, update):
     """
-    Auto-generate a test.yml file for a new module.
+    Generate nf-test snapshots for a module.
 
-    Given the name of a module, runs the Nextflow test command and automatically generate
-    the required `test.yml` file based on the output files.
+    Given the name of a module, runs the nf-test command to generate snapshots.
     """
-    from nf_core.modules import ModulesTestYmlBuilder
+    from nf_core.components.snapshot_generator import ComponentTestSnapshotGenerator
 
     try:
-        meta_builder = ModulesTestYmlBuilder(
-            module_name=tool,
+        snap_generator = ComponentTestSnapshotGenerator(
+            component_type="modules",
+            component_name=tool,
+            directory=dir,
             run_tests=run_tests,
-            test_yml_output_path=output,
-            force_overwrite=force,
             no_prompts=no_prompts,
+            update=update,
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
+            verbose=ctx.obj["verbose"],
         )
-        meta_builder.run()
+        snap_generator.run()
     except (UserWarning, LookupError) as e:
         log.critical(e)
         sys.exit(1)
@@ -1077,34 +1080,36 @@ def create_subworkflow(ctx, subworkflow, dir, author, force):
         sys.exit(1)
 
 
-# nf-core subworkflows create-test-yml
-@subworkflows.command("create-test-yml")
+# nf-core subworkflows create-snapshot
+@subworkflows.command("create-snapshot")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<nf-core/modules directory>")
 @click.option("-t", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
-@click.option("-o", "--output", type=str, help="Path for output YAML file")
-@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output YAML file if it already exists")
 @click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
-def create_test_yml(ctx, subworkflow, run_tests, output, force, no_prompts):
+@click.option("-u", "--update", is_flag=True, default=False, help="Update existing snapshots")
+def create_snapshot(ctx, subworkflow, dir, run_tests, no_prompts, update):
     """
     Auto-generate a test.yml file for a new subworkflow.
 
     Given the name of a module, runs the Nextflow test command and automatically generate
     the required `test.yml` file based on the output files.
     """
-    from nf_core.subworkflows import SubworkflowTestYmlBuilder
+    from nf_core.components.snapshot_generator import ComponentTestSnapshotGenerator
 
     try:
-        meta_builder = SubworkflowTestYmlBuilder(
-            subworkflow=subworkflow,
+        snap_generator = ComponentTestSnapshotGenerator(
+            component_type="subworkflows",
+            component_name=subworkflow,
+            directory=dir,
             run_tests=run_tests,
-            test_yml_output_path=output,
-            force_overwrite=force,
             no_prompts=no_prompts,
+            update=update,
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
+            verbose=ctx.obj["verbose"],
         )
-        meta_builder.run()
+        snap_generator.run()
     except (UserWarning, LookupError) as e:
         log.critical(e)
         sys.exit(1)
@@ -1344,7 +1349,7 @@ def install(ctx, subworkflow, dir, prompt, force, sha):
             ctx.obj["modules_repo_no_pull"],
         )
         exit_status = subworkflow_install.install(subworkflow)
-        if not exit_status and all:
+        if not exit_status and install_all:
             sys.exit(1)
     except (UserWarning, LookupError) as e:
         log.error(e)
@@ -1396,7 +1401,9 @@ def remove(ctx, dir, subworkflow):
 @click.option("-f", "--force", is_flag=True, default=False, help="Force update of subworkflow")
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the subworkflow")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install subworkflow at commit SHA")
-@click.option("-a", "--all", is_flag=True, default=False, help="Update all subworkflow installed in pipeline")
+@click.option(
+    "-a", "--all", "install_all", is_flag=True, default=False, help="Update all subworkflow installed in pipeline"
+)
 @click.option(
     "-x/-y",
     "--preview/--no-preview",
@@ -1419,7 +1426,7 @@ def remove(ctx, dir, subworkflow):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, subworkflow, dir, force, prompt, sha, all, preview, save_diff, update_deps):
+def update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 subworkflow within a pipeline.
 
@@ -1442,7 +1449,7 @@ def update(ctx, subworkflow, dir, force, prompt, sha, all, preview, save_diff, u
             ctx.obj["modules_repo_no_pull"],
         )
         exit_status = subworkflow_install.update(subworkflow)
-        if not exit_status and all:
+        if not exit_status and install_all:
             sys.exit(1)
     except (UserWarning, LookupError) as e:
         log.error(e)