Merge pull request #1665 from ErikDanielsson/gitlab-ci

Add CI testing for GitLab

.github/workflows/create-lint-wf.yml

@@ -96,6 +96,18 @@ jobs:
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
 
+      - name: nf-core modules install gitlab
+        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git install fastqc --dir nf-core-testpipeline/
+
+      - name: nf-core modules list local
+        run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+
+      - name: nf-core modules list remote
+        run: nf-core --log-file log.txt modules list remote
+
+      - name: nf-core modules list remote gitlab
+        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v2

CHANGELOG.md

@@ -23,6 +23,7 @@
 - Fix and improve broken test for Singularity container download ([#1622](https://github.com/nf-core/tools/pull/1622))
 - Use [`$XDG_CACHE_HOME`](https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html) or `~/.cache` instead of `$XDG_CONFIG_HOME` or `~/config/` as base directory for API cache
 - Switch CI to use [setup-nextflow](https://github.com/nf-core/setup-nextflow) action to install Nextflow ([#1650](https://github.com/nf-core/tools/pull/1650))
+- Add CI for GitLab remote [#1646](https://github.com/nf-core/tools/issues/1646)
 - Add `CITATION.cff` [#361](https://github.com/nf-core/tools/issues/361)
 - Allow customization of the `nf-core` pipeline template when using `nf-core create` ([#1548](https://github.com/nf-core/tools/issues/1548))
 

tests/modules/install.py

@@ -38,6 +38,11 @@ def test_modules_install_trimgalore_twice(self):
     assert self.mods_install.install("trimgalore") is True
 
 
+def test_modules_install_from_gitlab(self):
+    """Test installing a module from GitLab"""
+    assert self.mods_install_gitlab.install("fastqc") is True
+
+
 # TODO Remove comments once external repository to have same structure as nf-core/modules
 # def test_modules_install_trimgalore_alternative_source(self):
 #     """Test installing a module from a different source repository - TrimGalore!"""

tests/modules/list.py

@@ -13,6 +13,16 @@ def test_modules_list_remote(self):
     assert "fastqc" in output
 
 
+def test_modules_list_remote_gitlab(self):
+    """Test listing the modules in the remote gitlab repo"""
+    mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url="https://gitlab.com/nf-core/modules-test.git")
+    listed_mods = mods_list.list_modules()
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "fastqc" in output
+
+
 def test_modules_list_pipeline(self):
     """Test listing locally installed modules"""
     mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
@@ -33,3 +43,14 @@ def test_modules_install_and_list_pipeline(self):
     console.print(listed_mods)
     output = console.export_text()
     assert "trimgalore" in output
+
+
+def test_modules_install_gitlab_and_list_pipeline(self):
+    """Test listing locally installed modules"""
+    self.mods_install_gitlab.install("fastqc")
+    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+    listed_mods = mods_list.list_modules()
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "fastqc" in output

tests/test_modules.py

@@ -44,8 +44,14 @@ def setUp(self):
 
         # Set up install objects
         print("Setting up install objects")
-        self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
-        self.mods_install_alt = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=True, force=True)
+        self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True, no_pull=True)
+        self.mods_install_alt = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=True, force=True, no_pull=True)
+        self.mods_install_gitlab = nf_core.modules.ModuleInstall(
+            self.pipeline_dir,
+            prompt=False,
+            force=True,
+            remote_url="https://gitlab.com/nf-core/modules-test.git",
+        )
 
         # Set up remove objects
         print("Setting up remove objects")
@@ -92,6 +98,7 @@ def test_modulesrepo_class(self):
     )
     from .modules.install import (
         test_modules_install_emptypipeline,
+        test_modules_install_from_gitlab,
         test_modules_install_nomodule,
         test_modules_install_nopipeline,
         test_modules_install_trimgalore,
@@ -104,8 +111,10 @@ def test_modulesrepo_class(self):
     )
     from .modules.list import (
         test_modules_install_and_list_pipeline,
+        test_modules_install_gitlab_and_list_pipeline,
         test_modules_list_pipeline,
         test_modules_list_remote,
+        test_modules_list_remote_gitlab,
     )
     from .modules.module_test import (
         test_modules_test_check_inputs,