refactor: Split biocontainer and anaconda mocks

Responses actually throws an error if all the mocks aren't used. That
allowed me to clean up a few tests that weren't actually using the mocks
and find a few.

Author: edmundmiller

tests/modules/create.py

@@ -1,55 +1,47 @@
 import os
 
 import pytest
-import responses
 
 import nf_core.modules
-from tests.utils import mock_api_calls
 
 
 def test_modules_create_succeed(self):
     """Succeed at creating the TrimGalore! module"""
-    with responses.RequestsMock() as rsps:
-        mock_api_calls(rsps, "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()
+    # FIXME This should use the mock?
+    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"""
-    with responses.RequestsMock() as rsps:
-        mock_api_calls(rsps, "trim-galore", "0.6.7")
-        module_create = nf_core.modules.ModuleCreate(
-            self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
-        )
+    # FIXME This should use the mock?
+    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()
-        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"""
-    with responses.RequestsMock() as rsps:
-        mock_api_calls(rsps, "fastqc", "0.11.9")
-        module_create = nf_core.modules.ModuleCreate(
-            self.nfcore_modules, "fastqc", "@author", "process_low", False, False
-        )
-        module_create.create()
+    # FIXME This should use the mock?
+    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"""
-    with responses.RequestsMock() as rsps:
-        mock_api_calls(rsps, "star", "2.8.10a")
-        module_create = nf_core.modules.ModuleCreate(
-            self.nfcore_modules, "star/index", "@author", "process_medium", False, False
-        )
-        module_create.create()
+    # FIXME This should use the mock?
+    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

@@ -18,7 +18,6 @@
     GITLAB_URL,
     OLD_TRIMGALORE_BRANCH,
     OLD_TRIMGALORE_SHA,
-    mock_api_calls,
 )
 
 
@@ -34,12 +33,10 @@ 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", "org_path: nf-core", "\n"])
 
-    # mock biocontainers and anaconda response
-    with responses.RequestsMock() as rsps:
-        mock_api_calls(rsps, "bpipe", "0.9.11--hdfd78af_0")
-        # 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()
+    # FIXME Should use mock?
+    # 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/utils.py

@@ -70,11 +70,8 @@ def set_wd(path: Path):
         os.chdir(start_wd)
 
 
-def mock_api_calls(rsps: responses.RequestsMock, 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.split('--')[0]}"
-    )
+def mock_anaconda_api_calls(rsps: responses.RequestsMock, module, version):
+    """Mock anaconda api calls for module"""
     anaconda_api_url = f"https://api.anaconda.org/package/bioconda/{module}"
     anaconda_mock = {
         "latest_version": version.split("--")[0],
@@ -84,6 +81,14 @@ def mock_api_calls(rsps: responses.RequestsMock, module, version):
         "files": [{"version": version.split("--")[0]}],
         "license": "",
     }
+    rsps.get(anaconda_api_url, json=anaconda_mock, status=200)
+
+
+def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module, version):
+    """Mock biocontainers api calls for module"""
+    biocontainers_api_url = (
+        f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{module}/versions/{module}-{version.split('--')[0]}"
+    )
     biocontainers_mock = {
         "images": [
             {
@@ -98,5 +103,4 @@ def mock_api_calls(rsps: responses.RequestsMock, module, version):
             },
         ],
     }
-    rsps.get(anaconda_api_url, json=anaconda_mock, status=200)
     rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200)