Merge branch 'dev' into refgene-required-for-install

CHANGELOG.md

@@ -56,7 +56,7 @@
 - Add prompt for module name to `nf-core modules info` ([#1644](https://github.com/nf-core/tools/issues/1644))
 - Update docs with example of custom git remote ([#1645](https://github.com/nf-core/tools/issues/1645))
 - 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))
+- 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)) Removed after ([#1754](https://github.com/nf-core/tools/pull/1754))
 - Rename methods in `ModulesJson` to remove explicit reference to `modules.json`
 - Fix inconsistencies in the `--save-diff` flag `nf-core modules update`. Refactor `nf-core modules update` ([#1536](https://github.com/nf-core/tools/pull/1536))
 - Fix bug in `ModulesJson.check_up_to_date` causing it to ask for the remote of local modules

README.md

@@ -945,8 +945,6 @@ For example, if you want to install the `fastqc` module from the repository `nf-
 nf-core modules --git-remote [email protected]:nf-core/modules-test.git install fastqc
 ```
 
-If the modules in your custom remote are stored in another directory than `modules`, you can specify the path by using the `--base-path <path>` flag. This will default to `modules`. Note that all branches in a remote must use the same base path, otherwise the commands will fail.
-
 Note that a custom remote must follow a similar directory structure to that of `nf-core/moduleś` for the `nf-core modules` commands to work properly.
 
 The modules commands will during initalisation try to pull changes from the remote repositories. If you want to disable this, for example

nf_core/__main__.py

@@ -354,14 +354,8 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdow
     default=False,
     help="Do not pull in latest changes to local clone of modules repository.",
 )
-@click.option(
-    "--base-path",
-    type=str,
-    default=None,
-    help="Specify where the modules are stored in the remote",
-)
 @click.pass_context
-def modules(ctx, git_remote, branch, no_pull, base_path):
+def modules(ctx, git_remote, branch, no_pull):
     """
     Commands to manage Nextflow DSL2 modules (tool wrappers).
     """
@@ -373,7 +367,6 @@ def modules(ctx, git_remote, branch, no_pull, base_path):
     ctx.obj["modules_repo_url"] = git_remote
     ctx.obj["modules_repo_branch"] = branch
     ctx.obj["modules_repo_no_pull"] = no_pull
-    ctx.obj["modules_repo_base_path"] = base_path
 
 
 # nf-core modules list subcommands
@@ -402,7 +395,6 @@ def remote(ctx, keywords, json):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         print(module_list.list_modules(keywords, json))
     except (UserWarning, LookupError) as e:
@@ -433,7 +425,6 @@ def local(ctx, keywords, json, dir):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         print(module_list.list_modules(keywords, json))
     except (UserWarning, LookupError) as e:
@@ -470,7 +461,6 @@ def install(ctx, tool, dir, prompt, force, sha):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         exit_status = module_install.install(tool)
         if not exit_status and all:
@@ -528,7 +518,6 @@ def update(ctx, tool, dir, force, prompt, sha, all, preview, save_diff):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         exit_status = module_install.update(tool)
         if not exit_status and all:
@@ -562,7 +551,6 @@ def patch(ctx, tool, dir):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         module_patch.patch(tool)
     except (UserWarning, LookupError) as e:
@@ -591,7 +579,6 @@ def remove(ctx, dir, tool):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         module_remove.remove(tool)
     except (UserWarning, LookupError) as e:
@@ -695,7 +682,6 @@ def lint(ctx, tool, dir, key, all, fail_warned, local, passed, fix_version):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         module_lint.lint(
             module=tool,
@@ -746,7 +732,6 @@ def info(ctx, tool, dir):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         print(module_info.get_module_info())
     except (UserWarning, LookupError) as e:
@@ -772,7 +757,6 @@ def bump_versions(ctx, tool, dir, all, show_all):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            ctx.obj["modules_repo_base_path"],
         )
         version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
     except nf_core.modules.module_utils.ModuleException as e:

nf_core/modules/bump_versions.py

@@ -26,8 +26,8 @@
 
 
 class ModuleVersionBumper(ModuleCommand):
-    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, base_path=None):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull, base_path)
+    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False):
+        super().__init__(pipeline_dir, remote_url, branch, no_pull)
 
         self.up_to_date = None
         self.updated = None

nf_core/modules/info.py

@@ -55,8 +55,8 @@ class ModuleInfo(ModuleCommand):
         Take the parsed meta.yml and generate rich help
     """
 
-    def __init__(self, pipeline_dir, tool, remote_url, branch, no_pull, base_path):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull, base_path)
+    def __init__(self, pipeline_dir, tool, remote_url, branch, no_pull):
+        super().__init__(pipeline_dir, remote_url, branch, no_pull)
         self.meta = None
         self.local_path = None
         self.remote_location = None

nf_core/modules/install.py

@@ -23,19 +23,8 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
-        base_path=None,
     ):
-        # Check if we are given a base path, otherwise look in the modules.json
-        if base_path is None:
-            try:
-                modules_json = ModulesJson(pipeline_dir)
-                repo_name = nf_core.modules.module_utils.path_from_remote(remote_url)
-                base_path = modules_json.get_base_path(repo_name)
-            except:
-                # We don't want to fail yet if the modules.json is not found
-                pass
-
-        super().__init__(pipeline_dir, remote_url, branch, no_pull, base_path)
+        super().__init__(pipeline_dir, remote_url, branch, no_pull)
         self.force = force
         self.prompt = prompt
         self.sha = sha

nf_core/modules/lint/__init__.py

@@ -64,7 +64,7 @@ class ModuleLint(ModuleCommand):
     from .module_todos import module_todos
     from .module_version import module_version
 
-    def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull=False, base_path=None):
+    def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull=False):
         self.dir = dir
         try:
             self.dir, self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
@@ -75,7 +75,7 @@ def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull
         self.passed = []
         self.warned = []
         self.failed = []
-        self.modules_repo = ModulesRepo(remote_url, branch, no_pull, base_path)
+        self.modules_repo = ModulesRepo(remote_url, branch, no_pull)
         self.lint_tests = self.get_all_lint_tests(self.repo_type == "pipeline")
 
         if self.repo_type == "pipeline":

nf_core/modules/list.py

@@ -11,8 +11,8 @@
 
 
 class ModuleList(ModuleCommand):
-    def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False, base_path=None):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull, base_path)
+    def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False):
+        super().__init__(pipeline_dir, remote_url, branch, no_pull)
         self.remote = remote
 
     def list_modules(self, keywords=None, print_json=False):
@@ -103,7 +103,6 @@ def pattern_msg(keywords):
                             # pass repo_name to get info on modules even outside nf-core/modules
                             message, date = ModulesRepo(
                                 remote_url=repo_entry["git_url"],
-                                base_path=repo_entry["base_path"],
                                 branch=module_entry["branch"],
                             ).get_commit_info(version_sha)
                         except LookupError as e:

nf_core/modules/modules_command.py

@@ -19,11 +19,11 @@ class ModuleCommand:
     Base class for the 'nf-core modules' commands
     """
 
-    def __init__(self, dir, remote_url=None, branch=None, no_pull=False, base_path=None):
+    def __init__(self, dir, remote_url=None, branch=None, no_pull=False):
         """
         Initialise the ModulesCommand object
         """
-        self.modules_repo = ModulesRepo(remote_url, branch, no_pull, base_path)
+        self.modules_repo = ModulesRepo(remote_url, branch, no_pull)
         self.dir = dir
         try:
             if self.dir: