Bug fixes for '--force'

nf-core · ErikDanielsson · Jun 23, 2021 · Jun 16, 2021 · Jun 16, 2021 · Jun 16, 2021
commit dabdc642dd58421f72844e4c1c7e0409c3b3d7a0
diff --git a/nf_core/modules/module_utils.py b/nf_core/modules/module_utils.py
@@ -158,7 +158,7 @@ def local_module_equal_to_commit(local_files, module_name, modules_repo, commit_
     return all(files_are_equal)
 
 
-def prompt_module_version_sha(module, old_sha=None):
+def prompt_module_version_sha(module, installed_sha=None):
     older_commits_choice = questionary.Choice(
         title=[("fg:ansiyellow", "older commits"), ("class:choice-default", "")], value=""
     )
@@ -171,12 +171,10 @@ def prompt_module_version_sha(module, old_sha=None):
         choices = []
         for title, sha in map(lambda commit: (commit["trunc_message"], commit["git_sha"]), commits):
 
-            display_color = "fg:ansiblue" if sha != old_sha else "fg:ansired"
+            display_color = "fg:ansiblue" if sha != installed_sha else "fg:ansired"
             message = f"{title} {sha}"
-            if old_sha == sha:
-                message += " (old version)"
-            print(message)
-            print(sha, old_sha)
+            if installed_sha == sha:
+                message += " (installed version)"
             commit_display = [(display_color, message), ("class:choice-default", "")]
             choices.append(questionary.Choice(title=commit_display, value=sha))
         if len(next_page_commits) > 0:

diff --git a/nf_core/modules/pipeline_modules.py b/nf_core/modules/pipeline_modules.py
@@ -125,33 +125,44 @@ def install(self, module=None, latest=False, force=False):
             modules_json = json.load(fh)
 
         current_version = modules_json["modules"].get(module)
-        print(current_version)
+
         if current_version is not None:
             # Fetch the latest commit for the module
             git_log = get_module_git_log(module, per_page=1, page_nbr=1)
             if len(git_log) == 0:
                 log.error(f"Was unable to fetch version of module '{module}'")
                 return False
-            version = git_log[0]["git_sha"]
-            if current_version == version:
+            latest_version = git_log[0]["git_sha"]
+            if current_version == latest_version:
                 log.info("Already up to date")
                 return True
             elif not force:
                 log.error("Found newer version of module. To install use '--force'")
                 return False
-        if latest:
-            # Fetch the latest commit for the module
-            git_log = get_module_git_log(module, per_page=1, page_nbr=1)
-            if len(git_log) == 0:
-                log.error(f"Was unable to fetch version of module '{module}'")
-                return False
-            version = git_log[0]["git_sha"]
+
+            # Check for flag '--latest'
+            if latest:
+                version = latest_version
+            else:
+                try:
+                    version = prompt_module_version_sha(module, installed_sha=current_version["git_sha"])
+                except SystemError as e:
+                    log.error(e)
         else:
-            try:
-                version = prompt_module_version_sha(module, old_sha=current_version["git_sha"])
-            except SystemError as e:
-                log.error(e)
-                sys.exit(1)
+            # Check for flag '--latest'
+            if latest:
+                # Fetch the latest commit for the module
+                git_log = get_module_git_log(module, per_page=1, page_nbr=1)
+                if len(git_log) == 0:
+                    log.error(f"Was unable to fetch version of module '{module}'")
+                    return False
+                version = git_log[0]["git_sha"]
+            else:
+                try:
+                    version = prompt_module_version_sha(module)
+                except SystemError as e:
+                    log.error(e)
+                    sys.exit(1)
 
         # Check that we don't already have a folder for this module
         module_dir = os.path.join(self.pipeline_dir, "modules", *install_folder, module)