improve update.py

CHANGELOG.md

@@ -46,6 +46,7 @@
 - Command `nf-core modules test` obtains module name suggestions from installed modules ([#1624](https://github.com/nf-core/tools/pull/1624))
 - Add `--base-path` flag to `nf-core modules` to specify the base path for the modules in a remote. Also refactored `modules.json` code. ([#1643](https://github.com/nf-core/tools/issues/1643))
 - Rename methods in `ModulesJson` to remove explicit reference to `modules.json`
+- Fix inconsistencies in the `--show-diff` flag `nf-core modules update`. Refactor `nf-core modules update` ([#1536](https://github.com/nf-core/tools/pull/1536))
 
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 

nf_core/__main__.py

@@ -504,7 +504,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     help="Preview / no preview of changes before applying",
 )
 @click.option(
-    "-p",
+    "-D",
     "--save-diff",
     type=str,
     metavar="<filename>",

nf_core/modules/install.py

@@ -85,11 +85,10 @@ def install(self, module):
         current_version = modules_json.get_module_version(module, self.modules_repo.fullname)
 
         # Set the install folder based on the repository name
-        install_folder = [self.dir, "modules"]
-        install_folder.extend(os.path.split(self.modules_repo.fullname))
+        install_folder = os.path.join(self.dir, "modules", self.modules_repo.fullname)
 
         # Compute the module directory
-        module_dir = os.path.join(*install_folder, module)
+        module_dir = os.path.join(install_folder, module)
 
         # Check that the module is not already installed
         if (current_version is not None and os.path.exists(module_dir)) and not self.force:
@@ -135,7 +134,7 @@ def install(self, module):
 
         # Print include statement
         module_name = "_".join(module.upper().split("/"))
-        log.info(f"Include statement: include {{ {module_name} }} from '.{os.path.join(*install_folder, module)}/main'")
+        log.info(f"Include statement: include {{ {module_name} }} from '.{os.path.join(install_folder, module)}/main'")
 
         # Update module.json with newly installed module
         modules_json.update(self.modules_repo, module, version)

nf_core/modules/modules_json.py

@@ -301,7 +301,7 @@ def check_up_to_date(self):
                 base_path = contents["base_path"]
 
                 modules_repo = nf_core.modules.modules_repo.ModulesRepo(remote_url=remote, base_path=base_path)
-                install_folder = os.path.split(modules_repo.fullname)
+                install_dir = os.path.join(self.dir, "modules", modules_repo.fullname)
 
                 for module, entry in modules.items():
                     sha = entry.get("git_sha")
@@ -313,8 +313,7 @@ def check_up_to_date(self):
                         )
                         remove_from_mod_json[repo].append(module)
                         continue
-                    module_dir = [self.dir, "modules", *install_folder]
-                    if not modules_repo.install_module(module, module_dir, sha):
+                    if not modules_repo.install_module(module, install_dir, sha):
                         if repo not in remove_from_mod_json:
                             remove_from_mod_json[repo] = []
                         log.warning(f"Could not install module '{module}' in '{repo}' - removing from modules.json")

nf_core/modules/modules_repo.py

@@ -284,7 +284,7 @@ def install_module(self, module_name, install_dir, commit):
             return False
 
         # Copy the files from the repo to the install folder
-        shutil.copytree(self.get_module_dir(module_name), os.path.join(*install_dir, module_name))
+        shutil.copytree(self.get_module_dir(module_name), os.path.join(install_dir, module_name))
 
         # Switch back to the tip of the branch
         self.checkout_branch()
@@ -338,6 +338,12 @@ def get_module_git_log(self, module_name, depth=None, since="2021-07-07T00:00:00
         commits = ({"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits)
         return commits
 
+    def get_latest_module_version(self, module_name):
+        """
+        Returns the latest commit in the repository
+        """
+        return list(self.get_module_git_log(module_name, depth=1))[0]["git_sha"]
+
     def sha_exists_on_branch(self, sha):
         """
         Verifies that a given commit sha exists on the branch