Mock biocontainers and anaconda api calls in module tests

CHANGELOG.md

@@ -22,6 +22,7 @@
 - The default branch can now be specified when creating a new pipeline repo [#1959](https://github.com/nf-core/tools/pull/1959).
 - Only warn when checking that the pipeline directory contains a `main.nf` and a `nextflow.config` file if the pipeline is not an nf-core pipeline [#1964](https://github.com/nf-core/tools/pull/1964)
 - Add file `versions.yml` when generating `test.yml` with `nf-core modules create-test-yml` but don't check for md5sum [#1963](https://github.com/nf-core/tools/pull/1963)
+- Mock biocontainers and anaconda api calls in modules and subworkflows tests [#1967](https://github.com/nf-core/tools/pull/1967)
 
 ### Modules
 

requirements-dev.txt

@@ -6,3 +6,4 @@ pytest-cov
 pytest-datafiles
 Sphinx
 sphinx_rtd_theme
+requests_mock

tests/modules/create.py

@@ -1,43 +1,55 @@
 import os
 
 import pytest
+import requests_mock
 
 import nf_core.modules
+from tests.utils import mock_api_calls
 
 
 def test_modules_create_succeed(self):
     """Succeed at creating the TrimGalore! module"""
-    module_create = nf_core.modules.ModuleCreate(
-        self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
-    )
-    module_create.create()
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "trim-galore", "0.6.7")
+        module_create = nf_core.modules.ModuleCreate(
+            self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
+        )
+        module_create.create()
     assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf"))
 
 
 def test_modules_create_fail_exists(self):
     """Fail at creating the same module twice"""
-    module_create = nf_core.modules.ModuleCreate(
-        self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
-    )
-    module_create.create()
-    with pytest.raises(UserWarning) as excinfo:
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "trim-galore", "0.6.7")
+        module_create = nf_core.modules.ModuleCreate(
+            self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
+        )
         module_create.create()
+        with pytest.raises(UserWarning) as excinfo:
+            module_create.create()
     assert "Module file exists already" in str(excinfo.value)
 
 
 def test_modules_create_nfcore_modules(self):
     """Create a module in nf-core/modules clone"""
-    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "fastqc", "@author", "process_low", False, False)
-    module_create.create()
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "fastqc", "0.11.9")
+        module_create = nf_core.modules.ModuleCreate(
+            self.nfcore_modules, "fastqc", "@author", "process_low", False, False
+        )
+        module_create.create()
     assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf"))
     assert os.path.exists(os.path.join(self.nfcore_modules, "tests", "modules", "nf-core", "fastqc", "main.nf"))
 
 
 def test_modules_create_nfcore_modules_subtool(self):
     """Create a tool/subtool module in a nf-core/modules clone"""
-    module_create = nf_core.modules.ModuleCreate(
-        self.nfcore_modules, "star/index", "@author", "process_medium", False, False
-    )
-    module_create.create()
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "star", "2.8.10a")
+        module_create = nf_core.modules.ModuleCreate(
+            self.nfcore_modules, "star/index", "@author", "process_medium", False, False
+        )
+        module_create.create()
     assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf"))
     assert os.path.exists(os.path.join(self.nfcore_modules, "tests", "modules", "nf-core", "star", "index", "main.nf"))

tests/test_modules.py

@@ -7,6 +7,8 @@
 import tempfile
 import unittest
 
+import requests_mock
+
 import nf_core.create
 import nf_core.modules
 
@@ -17,6 +19,7 @@
     GITLAB_URL,
     OLD_TRIMGALORE_BRANCH,
     OLD_TRIMGALORE_SHA,
+    mock_api_calls,
 )
 
 
@@ -32,9 +35,12 @@ def create_modules_repo_dummy(tmp_dir):
     with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n"])
 
-    # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
-    module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False)
-    module_create.create()
+    # mock biocontainers and anaconda response
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "bpipe", "0.9.11")
+        # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
+        module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False)
+        module_create.create()
 
     return root_dir
 

tests/test_subworkflows.py

@@ -7,11 +7,13 @@
 import tempfile
 import unittest
 
+import requests_mock
+
 import nf_core.create
 import nf_core.modules
 import nf_core.subworkflows
 
-from .utils import GITLAB_URL
+from .utils import GITLAB_URL, mock_api_calls
 
 
 def create_modules_repo_dummy(tmp_dir):
@@ -29,9 +31,11 @@ def create_modules_repo_dummy(tmp_dir):
     with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n"])
 
-    # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
-    module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_medium", False, False)
-    module_create.create()
+    with requests_mock.Mocker() as mock:
+        mock_api_calls(mock, "bpipe", "0.9.11")
+        # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
+        module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_medium", False, False)
+        module_create.create()
 
     return root_dir
 

tests/utils.py

@@ -66,3 +66,22 @@ def set_wd(path: Path):
         yield
     finally:
         os.chdir(start_wd)
+
+
+def mock_api_calls(mock, module, version):
+    """Mock biocontainers and anaconda api calls for module"""
+    biocontainers_api_url = f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{module}/versions/{module}-{version}"
+    anaconda_api_url = f"https://api.anaconda.org/package/bioconda/{module}"
+    mock.register_uri("GET", biocontainers_api_url, text="to modify when the api works and I can know what to add")
+    anaconda_mock = {
+        "status_code": 200,
+        "latest_version": version,
+        "summary": "",
+        "doc_url": "",
+        "dev_url": "",
+        "files": [{"version": version}],
+        "license": "",
+    }
+    biocontainers_mock = {"status_code": 200, "images": [{"image_type": "Docker", "image_name": ""}]}
+    mock.register_uri("GET", anaconda_api_url, json=anaconda_mock)
+    mock.register_uri("GET", biocontainers_api_url, json=biocontainers_mock)