Use more pytest fixtures in modules tests

tests/conftest.py

@@ -0,0 +1,105 @@
+import os
+import re
+
+import pytest
+
+import nf_core.modules
+
+from .utils import (
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_BRANCH_TEST_OLD_SHA,
+    GITLAB_DEFAULT_BRANCH,
+    GITLAB_URL,
+    OLD_TRIMGALORE_BRANCH,
+    OLD_TRIMGALORE_SHA,
+)
+
+
+@pytest.fixture
+def tmp_dir(tmpdir):
+    return tmpdir
+
+
+@pytest.fixture
+def pipeline_dir(tmp_dir):
+    pipeline_dir = os.path.join(tmp_dir, "mypipeline")
+    nf_core.create.PipelineCreate(
+        "mypipeline", "it is mine", "me", no_git=True, outdir=pipeline_dir, plain=True
+    ).init_pipeline()
+    return pipeline_dir
+
+
+@pytest.fixture
+def modules_repo_dummy(tmp_dir):
+    """Create a dummy copy of the nf-core/modules repo"""
+
+    root_dir = os.path.join(tmp_dir, "modules")
+    os.makedirs(os.path.join(root_dir, "modules", "nf-core"))
+    os.makedirs(os.path.join(root_dir, "tests", "modules", "nf-core"))
+    os.makedirs(os.path.join(root_dir, "tests", "config"))
+    with open(os.path.join(root_dir, "tests", "config", "pytest_modules.yml"), "w") as fh:
+        fh.writelines(["test:", "\n  - modules/test/**", "\n  - tests/modules/test/**"])
+    with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
+        fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
+
+    # mock biocontainers and anaconda response
+    module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False)
+    module_create.create()
+
+    return root_dir
+
+
+@pytest.fixture
+def local_modules_repo(modules_repo_dummy, tmp_dir, pipeline_dir):
+    """Create a new PipelineSchema and Launch objects"""
+    component_type = "modules"
+
+    # Set up the schema
+    root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+    template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template")
+    # Set up install objects
+    mods_install = nf_core.modules.ModuleInstall(pipeline_dir, prompt=False, force=True)
+    mods_install_alt = nf_core.modules.ModuleInstall(pipeline_dir, prompt=True, force=True)
+    mods_install_old = nf_core.modules.ModuleInstall(
+        pipeline_dir,
+        prompt=False,
+        force=False,
+        sha=OLD_TRIMGALORE_SHA,
+        remote_url=GITLAB_URL,
+        branch=OLD_TRIMGALORE_BRANCH,
+    )
+    mods_install_trimgalore = nf_core.modules.ModuleInstall(
+        pipeline_dir,
+        prompt=False,
+        force=True,
+        remote_url=GITLAB_URL,
+        branch=OLD_TRIMGALORE_BRANCH,
+    )
+    mods_install_gitlab = nf_core.modules.ModuleInstall(
+        pipeline_dir,
+        prompt=False,
+        force=True,
+        remote_url=GITLAB_URL,
+        branch=GITLAB_DEFAULT_BRANCH,
+    )
+    mods_install_gitlab_old = nf_core.modules.ModuleInstall(
+        pipeline_dir,
+        prompt=False,
+        force=True,
+        remote_url=GITLAB_URL,
+        branch=GITLAB_BRANCH_TEST_BRANCH,
+        sha=GITLAB_BRANCH_TEST_OLD_SHA,
+    )
+
+    # Set up remove objects
+    mods_remove = nf_core.modules.ModuleRemove(pipeline_dir)
+    mods_remove_gitlab = nf_core.modules.ModuleRemove(
+        pipeline_dir,
+        remote_url=GITLAB_URL,
+        branch=GITLAB_DEFAULT_BRANCH,
+    )
+
+    # Set up the nf-core/modules repo dummy
+    nfcore_modules = modules_repo_dummy
+
+    return nfcore_modules

tests/test_modules/test_bump_versions.py

@@ -0,0 +1,51 @@
+import os
+import re
+
+import pytest
+
+import nf_core.modules
+from nf_core.modules.modules_utils import ModuleException
+
+
+def test_modules_bump_versions_single_module(local_modules_repo):
+    """Test updating a single module"""
+    # Change the bpipe/test version to an older version
+    print(local_modules_repo.__dir__())
+    main_nf_path = os.path.join(local_modules_repo, "modules", "nf-core", "bpipe", "test", "main.nf")
+    with open(main_nf_path, "r") as fh:
+        content = fh.read()
+    new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
+    with open(main_nf_path, "w") as fh:
+        fh.write(new_content)
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=local_modules_repo)
+    version_bumper.bump_versions(module="bpipe/test")
+    assert len(version_bumper.failed) == 0
+
+
+def test_modules_bump_versions_all_modules(local_modules_repo):
+    """Test updating all modules"""
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=local_modules_repo)
+    version_bumper.bump_versions(all_modules=True)
+    assert len(version_bumper.failed) == 0
+
+
+def test_modules_bump_versions_fail(local_modules_repo):
+    """Fail updating a module with wrong name"""
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=local_modules_repo)
+    with pytest.raises(ModuleException) as excinfo:
+        version_bumper.bump_versions(module="no/module")
+    assert "Could not find the specified module:" in str(excinfo.value)
+
+
+def test_modules_bump_versions_fail_unknown_version(local_modules_repo):
+    """Fail because of an unknown version"""
+    # Change the bpipe/test version to an older version
+    main_nf_path = os.path.join(local_modules_repo, "modules", "nf-core", "bpipe", "test", "main.nf")
+    with open(main_nf_path, "r") as fh:
+        content = fh.read()
+    new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content)
+    with open(main_nf_path, "w") as fh:
+        fh.write(new_content)
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=local_modules_repo)
+    version_bumper.bump_versions(module="bpipe/test")
+    assert "Conda package had unknown version" in version_bumper.failed[0][0]

tests/test_modules/test_create.py

@@ -0,0 +1,66 @@
+import os
+
+import pytest
+import requests_cache
+import responses
+
+import nf_core.modules
+
+from ..utils import mock_anaconda_api_calls, mock_biocontainers_api_calls
+
+
+def test_modules_create_succeed(pipeline_dir):
+    """Succeed at creating the TrimGalore! module"""
+    with responses.RequestsMock() as rsps:
+        mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
+        mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
+        module_create = nf_core.modules.ModuleCreate(
+            pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
+        )
+        with requests_cache.disabled():
+            module_create.create()
+    assert os.path.exists(os.path.join(pipeline_dir, "modules", "local", "trimgalore.nf"))
+
+
+def test_modules_create_fail_exists(pipeline_dir):
+    """Fail at creating the same module twice"""
+    with responses.RequestsMock() as rsps:
+        mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
+        mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
+        module_create = nf_core.modules.ModuleCreate(
+            pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
+        )
+        with requests_cache.disabled():
+            module_create.create()
+        with pytest.raises(UserWarning) as excinfo:
+            with requests_cache.disabled():
+                module_create.create()
+    assert "Module file exists already" in str(excinfo.value)
+
+
+def test_modules_create_nfcore_modules(local_modules_repo):
+    """Create a module in nf-core/modules clone"""
+    with responses.RequestsMock() as rsps:
+        mock_anaconda_api_calls(rsps, "fastqc", "0.11.9")
+        mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9")
+        module_create = nf_core.modules.ModuleCreate(
+            local_modules_repo, "fastqc", "@author", "process_low", False, False
+        )
+        with requests_cache.disabled():
+            module_create.create()
+    assert os.path.exists(os.path.join(local_modules_repo, "modules", "nf-core", "fastqc", "main.nf"))
+    assert os.path.exists(os.path.join(local_modules_repo, "tests", "modules", "nf-core", "fastqc", "main.nf"))
+
+
+def test_modules_create_nfcore_modules_subtool(local_modules_repo):
+    """Create a tool/subtool module in a nf-core/modules clone"""
+    with responses.RequestsMock() as rsps:
+        mock_anaconda_api_calls(rsps, "star", "2.8.10a")
+        mock_biocontainers_api_calls(rsps, "star", "2.8.10a")
+        module_create = nf_core.modules.ModuleCreate(
+            local_modules_repo, "star/index", "@author", "process_medium", False, False
+        )
+        with requests_cache.disabled():
+            module_create.create()
+    assert os.path.exists(os.path.join(local_modules_repo, "modules", "nf-core", "star", "index", "main.nf"))
+    assert os.path.exists(os.path.join(local_modules_repo, "tests", "modules", "nf-core", "star", "index", "main.nf"))