created draft for test file

tests/subworkflows/patch.py

@@ -0,0 +1,77 @@
+import os
+
+import pytest
+
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.subworkflows.install import SubworkflowInstall
+
+from ..utils import (
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_REPO,
+    GITLAB_SUBWORKFLOWS_BRANCH,
+    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
+    GITLAB_URL,
+    with_temporary_folder,
+)
+
+"""
+Test the 'nf-core subworkflows patch' command
+"""
+
+def setup_patch(self, pipeline_dir, modify_subworkflow):
+    # Install the subworkflow bam_sort_stats_samtools
+    subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
+    sub_subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools")
+    samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+    samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort")
+    samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+    samtools_idxstats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats")
+    samtools_flagstat_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat")
+
+
+    if modify_subworkflow:
+        # Modify the subworkflow
+        subworkflow_path = Path(pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
+        modify_subworkflow(subworkflow_path / "main.nf")
+
+
+def modify_subworkflow(path):
+    """Modify a file to test patch creation"""
+    with open(path) as fh:
+        lines = fh.readlines()
+    # We want a patch file that looks something like:
+    # -    ch_fasta // channel: [ val(meta), path(fasta) ]
+    for line_index in range(len(lines)):
+        if lines[line_index] == "    ch_fasta // channel: [ val(meta), path(fasta) ]\n":
+            to_pop = line_index
+    lines.pop(to_pop)
+    with open(path, "w") as fh:
+        fh.writelines(lines)
+
+def test_create_patch_change(self):
+    """Test creating a patch when there is a change to the module"""
+
+def test_create_patch_no_change(self):
+    """Test creating a patch when there is no change to the subworkflow"""
+    # Try creating a patch file
+    # Check that no patch file has been added to the directory
+
+def test_create_patch_try_apply_failed(self):
+    """Test creating a patch file and applying it to a new version of the the files"""
+
+def test_create_patch_try_apply_successful(self):
+    """Test creating a patch file and applying it to a new version of the the files"""
+
+def test_create_patch_update_fail(self):
+    """Test creating a patch file and updating a subworkflow when there is a diff conflict"""
+
+def test_create_patch_update_success (self):
+    """
+    Test creating a patch file and the updating the subworkflow
+
+    Should have the same effect as 'test_create_patch_try_apply_successful'
+    but uses higher level api
+    """
+
+def test_remove_patch(self):
+    """Test creating a patch when there is no change to the subworkflow"""