From 64c684ca4d91edc34448d858a448bc2dde8861d3 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 12:29:00 +0200
Subject: [PATCH 01/28] increase worflow linting

---
 planemo/commands/cmd_workflow_lint.py |  6 ++
 planemo/lint.py                       |  2 +
 planemo/workflow_lint.py              | 92 +++++++++++++++++++++++++--
 3 files changed, 96 insertions(+), 4 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 80085c46d..64f9c1cc6 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -14,6 +14,12 @@
 @options.report_xunit()
 @options.fail_level_option()
 @options.skip_option()
+@click.option(
+    "--iwc",
+    is_flag=True,
+    default=False,
+    help="Check workflows directory with the standards of iwc",
+)
 @command_function
 def cli(ctx, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
diff --git a/planemo/lint.py b/planemo/lint.py
index 5b85022de..d0c302f50 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -18,6 +18,7 @@ def build_lint_args(ctx, **kwds):
     """Handle common report, error, and skip linting arguments."""
     report_level = kwds.get("report_level", "all")
     fail_level = kwds.get("fail_level", "warn")
+    iwc_grade = kwds.get("iwc", False)
     skip = kwds.get("skip", None)
     if skip is None:
         skip = ctx.global_config.get("lint_skip", "")
@@ -42,6 +43,7 @@ def build_lint_args(ctx, **kwds):
         level=report_level,
         fail_level=fail_level,
         skip_types=skip_types,
+        iwc_grade=iwc_grade,
     )
     return lint_args
 
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index fdc2bbc80..f34f0195e 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -57,6 +57,8 @@ class WorkflowLintContext(LintContext):
     # Setup training topic for linting - probably should pass this through
     # from click arguments.
     training_topic = None
+    release = None
+    iwc_grade = False
 
 
 def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
@@ -138,6 +140,13 @@ def lint_workflow_artifacts_on_paths(
 def _lint_workflow_artifacts_on_path(
     lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
 ) -> None:
+    if lint_args['iwc_grade']:
+        if not os.path.isdir(path):
+            raise ValueError("iwc standards can only be checked on directories.")
+        lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
+        lint_context.lint("lint_changelog", _lint_changelog_version, path)
+        lint_context.iwc_grade = True
+
     for potential_workflow_artifact_path in find_potential_workflow_files(path):
         if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:
             lint_context.lint("lint_dockstore", _lint_dockstore_config, potential_workflow_artifact_path)
@@ -150,8 +159,10 @@ def structure(path, lint_context):
                 workflow_class = workflow_dict.get("class")
                 lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
                 lint_func(lint_context, workflow_dict, path=path)
-
+            
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
+            if lint_context.iwc_grade and lint_context.version is not None:
+                lint_context.lint("lint_version", check_version, potential_workflow_artifact_path)
             lint_context.lint("lint_best_practices", _lint_best_practices, potential_workflow_artifact_path)
             lint_context.lint("lint_tests", _lint_tsts, potential_workflow_artifact_path)
             lint_context.lint("lint_tool_ids", _lint_tool_ids, potential_workflow_artifact_path)
@@ -394,6 +405,11 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
         lint_context.error("Invalid YAML contents found in %s" % DOCKSTORE_REGISTRY_CONF)
         return
 
+    if "version" not in dockstore_yaml:
+        lint_context.error("Invalid YAML contents found in %s, no version defined" % DOCKSTORE_REGISTRY_CONF)
+    if dockstore_yaml.get("version") != DOCKSTORE_REGISTRY_CONF_VERSION:
+        lint_context.error("Invalid YAML version found in %s." % DOCKSTORE_REGISTRY_CONF)
+
     if "workflows" not in dockstore_yaml:
         lint_context.error("Invalid YAML contents found in %s, no workflows defined" % DOCKSTORE_REGISTRY_CONF)
         return
@@ -403,8 +419,16 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
         lint_context.error("Invalid YAML contents found in %s, workflows not a list" % DOCKSTORE_REGISTRY_CONF)
         return
 
+    if len(workflow_entries) == 0:
+        lint_context.error("No workflow specified in the .dockstore.yml.")
+
+    workflow_names_in_dockstore = []
     for workflow_entry in workflow_entries:
         _lint_dockstore_workflow_entry(lint_context, os.path.dirname(path), workflow_entry)
+        workflow_name = workflow_entry.get("name")
+        if workflow_name in workflow_names_in_dockstore:
+            lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} has multiple workflow entries with the same name")
+        workflow_names_in_dockstore.append(workflow_name)
 
 
 def _lint_dockstore_workflow_entry(
@@ -415,20 +439,26 @@ def _lint_dockstore_workflow_entry(
         return
 
     found_errors = False
-    for required_key in ["primaryDescriptorPath", "subclass"]:
+    for required_key in ["primaryDescriptorPath", "subclass", "name"]:
         if required_key not in workflow_entry:
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing required key {required_key}")
             found_errors = True
 
+    if lint_context.iwc_grade:
+        lint_fun = lint_context.error
+    else:
+        lint_fun = lint_context.warn
     for recommended_key in ["testParameterFiles"]:
         if recommended_key not in workflow_entry:
-            lint_context.warn(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
+            lint_fun(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
 
     if found_errors:
         # Don't do the rest of the validation for a broken file.
         return
 
-    # TODO: validate subclass
+    if workflow_entry.get("subclass") != "Galaxy":
+        lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry subclass must be 'Galaxy'.")
+
     descriptor_path = workflow_entry["primaryDescriptorPath"]
     test_files = workflow_entry.get("testParameterFiles", [])
 
@@ -437,6 +467,24 @@ def _lint_dockstore_workflow_entry(
         if not os.path.exists(referenced_path):
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry references absent file {referenced_file}")
 
+    # Check there is no space in name:
+    workflow_name = workflow_entry.get("name")
+    # Check the name has no space
+    if ' ' in workflow_name:
+        lint_context.error("Dockstore does not accept workflow names with space.",
+                           f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.")
+
+    # Check there is at least one author
+    if len(workflow_entry.get('authors')) == 0:
+        lint_fun(f"Workflow {workflow_name} should have no " \
+                            "'authors' in the .dockstore.yml.")
+    # Check there is not mailto
+    for author in workflow_entry.get('authors'):
+        if 'email' in author:
+            if author['email'].startswith('mailto:'):
+                lint_context.error("email field of the .dockstore.yml must not "
+                                "contain 'mailto:'")
+
 
 def looks_like_a_workflow(path: str) -> bool:
     """Return boolean indicating if this path looks like a workflow."""
@@ -537,3 +585,39 @@ def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: T
     if not failed:
         lint_context.valid("All tool ids appear to be valid.")
     return None
+
+def _lint_required_files_workflow_dir(path: str, lint_context: WorkflowLintContext) -> None:
+    # Check all required files are present
+    required_files = \
+        ['README.md', 'CHANGELOG.md', '.dockstore.yml']
+    for required_file in required_files:
+        if not os.path.exists(os.path.join(path, required_file)):
+            lint_context.error(f"The file {required_file} is" \
+                            " missing but required.")
+
+def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
+    lint_context.version = None
+    # Check the version can be get from the CHANGELOG.md
+    if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
+        return
+    with open(os.path.join(path, 'CHANGELOG.md'), 'r') as f:
+        for line in f:
+            if line.startswith('## ['):
+                lint_context.version = line.split(']')[0].replace('## [', '')
+                break
+
+    if lint_context.version is None:
+        lint_context.error("No version found in CHANGELOG. " \
+                           "The version should be in a line that starts like " \
+                           "'## [version number]'")
+
+
+def check_version(path, lint_context):
+    with open(path) as f:
+        workflow_dict = ordered_load(f)
+    if 'release' not in workflow_dict:
+        lint_context.error(f"The workflow {path} has no release")
+    else:
+        if lint_context.version is not None and workflow_dict.get("release") != lint_context.version:
+            lint_context.error(f"The release of workflow {file} does not match " \
+                                "the version in the CHANGELOG.")

From af6758e5e81e60ed02edbbbeef868afd76dc0842 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 12:39:22 +0200
Subject: [PATCH 02/28] linting

---
 planemo/workflow_lint.py | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index f34f0195e..487311d49 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -159,7 +159,7 @@ def structure(path, lint_context):
                 workflow_class = workflow_dict.get("class")
                 lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
                 lint_func(lint_context, workflow_dict, path=path)
-            
+
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
             if lint_context.iwc_grade and lint_context.version is not None:
                 lint_context.lint("lint_version", check_version, potential_workflow_artifact_path)
@@ -476,14 +476,13 @@ def _lint_dockstore_workflow_entry(
 
     # Check there is at least one author
     if len(workflow_entry.get('authors')) == 0:
-        lint_fun(f"Workflow {workflow_name} should have no " \
-                            "'authors' in the .dockstore.yml.")
+        lint_fun(f"Workflow {workflow_name} should have no "
+                 "'authors' in the .dockstore.yml.")
     # Check there is not mailto
     for author in workflow_entry.get('authors'):
-        if 'email' in author:
-            if author['email'].startswith('mailto:'):
-                lint_context.error("email field of the .dockstore.yml must not "
-                                "contain 'mailto:'")
+        if author.get('email', '').startswith('mailto:'):
+            lint_context.error("email field of the .dockstore.yml must not "
+                               "contain 'mailto:'")
 
 
 def looks_like_a_workflow(path: str) -> bool:
@@ -586,14 +585,16 @@ def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: T
         lint_context.valid("All tool ids appear to be valid.")
     return None
 
+
 def _lint_required_files_workflow_dir(path: str, lint_context: WorkflowLintContext) -> None:
     # Check all required files are present
     required_files = \
         ['README.md', 'CHANGELOG.md', '.dockstore.yml']
     for required_file in required_files:
         if not os.path.exists(os.path.join(path, required_file)):
-            lint_context.error(f"The file {required_file} is" \
-                            " missing but required.")
+            lint_context.error(f"The file {required_file} is"
+                               " missing but required.")
+
 
 def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
     lint_context.version = None
@@ -607,8 +608,8 @@ def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> Non
                 break
 
     if lint_context.version is None:
-        lint_context.error("No version found in CHANGELOG. " \
-                           "The version should be in a line that starts like " \
+        lint_context.error("No version found in CHANGELOG. "
+                           "The version should be in a line that starts like "
                            "'## [version number]'")
 
 
@@ -619,5 +620,5 @@ def check_version(path, lint_context):
         lint_context.error(f"The workflow {path} has no release")
     else:
         if lint_context.version is not None and workflow_dict.get("release") != lint_context.version:
-            lint_context.error(f"The release of workflow {file} does not match " \
-                                "the version in the CHANGELOG.")
+            lint_context.error(f"The release of workflow {path} does not match "
+                               "the version in the CHANGELOG.")

From 1d61ca1b8c0c05909a49fcf72daa2cc771f07fc8 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 14:38:40 +0200
Subject: [PATCH 03/28] restore build_lint_args

---
 planemo/commands/cmd_workflow_lint.py | 1 +
 planemo/lint.py                       | 2 --
 planemo/workflow_lint.py              | 6 +++---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 64f9c1cc6..d226f40f7 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -29,5 +29,6 @@ def cli(ctx, paths, **kwds):
         ctx,
         paths,
         lint_args,
+        iwc_grade = kwds.get("iwc", False)
     )
     ctx.exit(exit_code)
diff --git a/planemo/lint.py b/planemo/lint.py
index d0c302f50..5b85022de 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -18,7 +18,6 @@ def build_lint_args(ctx, **kwds):
     """Handle common report, error, and skip linting arguments."""
     report_level = kwds.get("report_level", "all")
     fail_level = kwds.get("fail_level", "warn")
-    iwc_grade = kwds.get("iwc", False)
     skip = kwds.get("skip", None)
     if skip is None:
         skip = ctx.global_config.get("lint_skip", "")
@@ -43,7 +42,6 @@ def build_lint_args(ctx, **kwds):
         level=report_level,
         fail_level=fail_level,
         skip_types=skip_types,
-        iwc_grade=iwc_grade,
     )
     return lint_args
 
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 487311d49..12ad9f690 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -124,10 +124,11 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
 
 
 def lint_workflow_artifacts_on_paths(
-    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]
+    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]], iwc_grade: bool
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
+    lint_context.iwc_grade = iwc_grade
     for path in paths:
         _lint_workflow_artifacts_on_path(lint_context, path, lint_args)
 
@@ -140,12 +141,11 @@ def lint_workflow_artifacts_on_paths(
 def _lint_workflow_artifacts_on_path(
     lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
 ) -> None:
-    if lint_args['iwc_grade']:
+    if lint_context.iwc_grade:
         if not os.path.isdir(path):
             raise ValueError("iwc standards can only be checked on directories.")
         lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
         lint_context.lint("lint_changelog", _lint_changelog_version, path)
-        lint_context.iwc_grade = True
 
     for potential_workflow_artifact_path in find_potential_workflow_files(path):
         if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:

From dd9b1bb227dfac02e30571307c4735b6cb784d2d Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 14:57:21 +0200
Subject: [PATCH 04/28] fix cases with no authors in dockstore.yml

---
 planemo/workflow_lint.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 12ad9f690..dbcc94b74 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -475,11 +475,11 @@ def _lint_dockstore_workflow_entry(
                            f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.")
 
     # Check there is at least one author
-    if len(workflow_entry.get('authors')) == 0:
-        lint_fun(f"Workflow {workflow_name} should have no "
+    if len(workflow_entry.get('authors', [])) == 0:
+        lint_fun(f"Workflow {workflow_name} have no "
                  "'authors' in the .dockstore.yml.")
     # Check there is not mailto
-    for author in workflow_entry.get('authors'):
+    for author in workflow_entry.get('authors', []):
         if author.get('email', '').startswith('mailto:'):
             lint_context.error("email field of the .dockstore.yml must not "
                                "contain 'mailto:'")

From f7401d8fe7b2df86e731c90755f8e880d43f25e1 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 14:57:45 +0200
Subject: [PATCH 05/28] fix DOCKSTORE_REGISTRY_CONF_VERSION

---
 planemo/workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index dbcc94b74..6c1c2fea5 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -407,7 +407,7 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
 
     if "version" not in dockstore_yaml:
         lint_context.error("Invalid YAML contents found in %s, no version defined" % DOCKSTORE_REGISTRY_CONF)
-    if dockstore_yaml.get("version") != DOCKSTORE_REGISTRY_CONF_VERSION:
+    if str(dockstore_yaml.get("version")) != DOCKSTORE_REGISTRY_CONF_VERSION:
         lint_context.error("Invalid YAML version found in %s." % DOCKSTORE_REGISTRY_CONF)
 
     if "workflows" not in dockstore_yaml:

From d4ae50fc7155cd9319bd2a0a869fd8eb944141f7 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 14:58:07 +0200
Subject: [PATCH 06/28] change name from required to recommanded

---
 planemo/workflow_lint.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 6c1c2fea5..116ff8872 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -425,7 +425,7 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
     workflow_names_in_dockstore = []
     for workflow_entry in workflow_entries:
         _lint_dockstore_workflow_entry(lint_context, os.path.dirname(path), workflow_entry)
-        workflow_name = workflow_entry.get("name")
+        workflow_name = workflow_entry.get("name", "")
         if workflow_name in workflow_names_in_dockstore:
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} has multiple workflow entries with the same name")
         workflow_names_in_dockstore.append(workflow_name)
@@ -439,7 +439,7 @@ def _lint_dockstore_workflow_entry(
         return
 
     found_errors = False
-    for required_key in ["primaryDescriptorPath", "subclass", "name"]:
+    for required_key in ["primaryDescriptorPath", "subclass"]:
         if required_key not in workflow_entry:
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing required key {required_key}")
             found_errors = True
@@ -448,7 +448,7 @@ def _lint_dockstore_workflow_entry(
         lint_fun = lint_context.error
     else:
         lint_fun = lint_context.warn
-    for recommended_key in ["testParameterFiles"]:
+    for recommended_key in ["testParameterFiles", "name"]:
         if recommended_key not in workflow_entry:
             lint_fun(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
 

From 619cae9ce20f7881a89ddf73e80069293a8d3140 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 15:01:58 +0200
Subject: [PATCH 07/28] linting

---
 planemo/commands/cmd_workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index d226f40f7..79ac6d305 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -29,6 +29,6 @@ def cli(ctx, paths, **kwds):
         ctx,
         paths,
         lint_args,
-        iwc_grade = kwds.get("iwc", False)
+        iwc_grade=kwds.get("iwc", False)
     )
     ctx.exit(exit_code)

From eb86e3b8bed425802990da90bb827e6d474777c7 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Sat, 29 Jun 2024 15:12:20 +0200
Subject: [PATCH 08/28] fix forgotten consequence of name from required to
 recommanded

---
 planemo/workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 116ff8872..91ed64f29 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -468,7 +468,7 @@ def _lint_dockstore_workflow_entry(
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry references absent file {referenced_file}")
 
     # Check there is no space in name:
-    workflow_name = workflow_entry.get("name")
+    workflow_name = workflow_entry.get("name", "")
     # Check the name has no space
     if ' ' in workflow_name:
         lint_context.error("Dockstore does not accept workflow names with space.",

From 5516443ef37d30ef6e94fca8055db0f44733ecda Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 10:26:33 +0200
Subject: [PATCH 09/28] put iwc_grade in lint_args as suggested by
 @bernt-matthias

---
 planemo/commands/cmd_workflow_lint.py | 4 ++--
 planemo/workflow_lint.py              | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 79ac6d305..132e84d99 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -25,10 +25,10 @@ def cli(ctx, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
     lint_args = build_lint_args(ctx, **kwds)
+    lint_args["iwc_grade"] = kwds.get("iwc", False)
     exit_code = lint_workflow_artifacts_on_paths(
         ctx,
         paths,
-        lint_args,
-        iwc_grade=kwds.get("iwc", False)
+        lint_args
     )
     ctx.exit(exit_code)
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 91ed64f29..91346e4d2 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -124,11 +124,11 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
 
 
 def lint_workflow_artifacts_on_paths(
-    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]], iwc_grade: bool
+    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
-    lint_context.iwc_grade = iwc_grade
+    lint_context.iwc_grade = lint_args["iwc_grade"]
     for path in paths:
         _lint_workflow_artifacts_on_path(lint_context, path, lint_args)
 

From 8639d1dc9adb5de58fa344ec866e64e2c6277221 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 11:45:23 +0200
Subject: [PATCH 10/28] remove release/version from WorkflowLintContext as
 suggested by @matthias-bernt

---
 planemo/workflow_lint.py | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 91346e4d2..c618dfe58 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -57,7 +57,6 @@ class WorkflowLintContext(LintContext):
     # Setup training topic for linting - probably should pass this through
     # from click arguments.
     training_topic = None
-    release = None
     iwc_grade = False
 
 
@@ -161,8 +160,8 @@ def structure(path, lint_context):
                 lint_func(lint_context, workflow_dict, path=path)
 
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
-            if lint_context.iwc_grade and lint_context.version is not None:
-                lint_context.lint("lint_version", check_version, potential_workflow_artifact_path)
+            if lint_context.iwc_grade:
+                lint_context.lint("lint_release", _lint_release, potential_workflow_artifact_path)
             lint_context.lint("lint_best_practices", _lint_best_practices, potential_workflow_artifact_path)
             lint_context.lint("lint_tests", _lint_tsts, potential_workflow_artifact_path)
             lint_context.lint("lint_tool_ids", _lint_tool_ids, potential_workflow_artifact_path)
@@ -596,29 +595,37 @@ def _lint_required_files_workflow_dir(path: str, lint_context: WorkflowLintConte
                                " missing but required.")
 
 
-def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
-    lint_context.version = None
-    # Check the version can be get from the CHANGELOG.md
+def _get_changelog_version(path: str) -> str:
+    # Get the version from the CHANGELOG.md
+    version = ""
     if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
-        return
+        return version
     with open(os.path.join(path, 'CHANGELOG.md'), 'r') as f:
         for line in f:
             if line.startswith('## ['):
-                lint_context.version = line.split(']')[0].replace('## [', '')
+                version = line.split(']')[0].replace('## [', '')
                 break
+    return version
+
 
-    if lint_context.version is None:
+def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
+    # Check the version can be get from the CHANGELOG.md
+    if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
+        return
+    if _get_changelog_version(path) == "":
         lint_context.error("No version found in CHANGELOG. "
                            "The version should be in a line that starts like "
                            "'## [version number]'")
 
 
-def check_version(path, lint_context):
+def _lint_release(path, lint_context):
     with open(path) as f:
         workflow_dict = ordered_load(f)
     if 'release' not in workflow_dict:
         lint_context.error(f"The workflow {path} has no release")
     else:
-        if lint_context.version is not None and workflow_dict.get("release") != lint_context.version:
+        # Try to get the version from the CHANGELOG:
+        version = _get_changelog_version(os.path.join(os.path.dirname(path), "CHANGELOG.md"))
+        if version != "" and workflow_dict.get("release") != version:
             lint_context.error(f"The release of workflow {path} does not match "
                                "the version in the CHANGELOG.")

From 5c19e56d2dc64a1d71c2ce1abb44bc33415197b7 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 12:00:06 +0200
Subject: [PATCH 11/28] fix type of lint_args

---
 planemo/commands/cmd_workflow_lint.py | 2 +-
 planemo/workflow_lint.py              | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 132e84d99..5cdf0c4e1 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -25,7 +25,7 @@ def cli(ctx, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
     lint_args = build_lint_args(ctx, **kwds)
-    lint_args["iwc_grade"] = kwds.get("iwc", False)
+    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
     exit_code = lint_workflow_artifacts_on_paths(
         ctx,
         paths,
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index c618dfe58..81369c2cf 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -127,7 +127,7 @@ def lint_workflow_artifacts_on_paths(
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
-    lint_context.iwc_grade = lint_args["iwc_grade"]
+    lint_context.iwc_grade = lint_args["iwc_grade"] == "True"
     for path in paths:
         _lint_workflow_artifacts_on_path(lint_context, path, lint_args)
 

From 302c504722c9d3edfc9e0b8a22b5c58e8ff9e3e6 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 13:01:59 +0200
Subject: [PATCH 12/28] remove iwc_grade from WorkflowLintContext and add
 lint_dockstore_best_practices

---
 planemo/workflow_lint.py | 54 ++++++++++++++++++++++++++++------------
 1 file changed, 38 insertions(+), 16 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 81369c2cf..389457199 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -57,7 +57,6 @@ class WorkflowLintContext(LintContext):
     # Setup training topic for linting - probably should pass this through
     # from click arguments.
     training_topic = None
-    iwc_grade = False
 
 
 def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
@@ -127,7 +126,6 @@ def lint_workflow_artifacts_on_paths(
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
-    lint_context.iwc_grade = lint_args["iwc_grade"] == "True"
     for path in paths:
         _lint_workflow_artifacts_on_path(lint_context, path, lint_args)
 
@@ -140,7 +138,8 @@ def lint_workflow_artifacts_on_paths(
 def _lint_workflow_artifacts_on_path(
     lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
 ) -> None:
-    if lint_context.iwc_grade:
+    iwc_grade = lint_args["iwc_grade"] == "True"
+    if iwc_grade:
         if not os.path.isdir(path):
             raise ValueError("iwc standards can only be checked on directories.")
         lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
@@ -149,6 +148,8 @@ def _lint_workflow_artifacts_on_path(
     for potential_workflow_artifact_path in find_potential_workflow_files(path):
         if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:
             lint_context.lint("lint_dockstore", _lint_dockstore_config, potential_workflow_artifact_path)
+            if iwc_grade:
+                lint_context.lint("lint_dockstore_best_practices", _lint_dockstore_config_best_practices, potential_workflow_artifact_path)
 
         elif looks_like_a_workflow(potential_workflow_artifact_path):
 
@@ -160,7 +161,7 @@ def structure(path, lint_context):
                 lint_func(lint_context, workflow_dict, path=path)
 
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
-            if lint_context.iwc_grade:
+            if iwc_grade:
                 lint_context.lint("lint_release", _lint_release, potential_workflow_artifact_path)
             lint_context.lint("lint_best_practices", _lint_best_practices, potential_workflow_artifact_path)
             lint_context.lint("lint_tests", _lint_tsts, potential_workflow_artifact_path)
@@ -443,14 +444,6 @@ def _lint_dockstore_workflow_entry(
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing required key {required_key}")
             found_errors = True
 
-    if lint_context.iwc_grade:
-        lint_fun = lint_context.error
-    else:
-        lint_fun = lint_context.warn
-    for recommended_key in ["testParameterFiles", "name"]:
-        if recommended_key not in workflow_entry:
-            lint_fun(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
-
     if found_errors:
         # Don't do the rest of the validation for a broken file.
         return
@@ -473,10 +466,6 @@ def _lint_dockstore_workflow_entry(
         lint_context.error("Dockstore does not accept workflow names with space.",
                            f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.")
 
-    # Check there is at least one author
-    if len(workflow_entry.get('authors', [])) == 0:
-        lint_fun(f"Workflow {workflow_name} have no "
-                 "'authors' in the .dockstore.yml.")
     # Check there is not mailto
     for author in workflow_entry.get('authors', []):
         if author.get('email', '').startswith('mailto:'):
@@ -629,3 +618,36 @@ def _lint_release(path, lint_context):
         if version != "" and workflow_dict.get("release") != version:
             lint_context.error(f"The release of workflow {path} does not match "
                                "the version in the CHANGELOG.")
+
+
+def _lint_dockstore_config_best_practices(path: str, lint_context: WorkflowLintContext) -> None:
+    dockstore_yaml = None
+    try:
+        with open(path) as f:
+            dockstore_yaml = yaml.safe_load(f)
+    except Exception:
+        return
+    
+    if not isinstance(dockstore_yaml, dict):
+        return
+
+    workflow_entries = dockstore_yaml.get("workflows")
+    if not isinstance(workflow_entries, list):
+        return
+
+    for workflow_entry in workflow_entries:
+        _lint_dockstore_workflow_entry_best_practices(lint_context, os.path.dirname(path), workflow_entry)
+
+
+def _lint_dockstore_workflow_entry_best_practices(
+    lint_context: WorkflowLintContext, directory: str, workflow_entry: Dict[str, Any]
+) -> None:
+    for recommended_key in ["testParameterFiles", "name"]:
+        if recommended_key not in workflow_entry:
+            lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
+
+    workflow_name = workflow_entry.get("name", "")
+    # Check there is at least one author
+    if len(workflow_entry.get('authors', [])) == 0:
+        lint_context.error(f"Workflow {workflow_name} have no "
+                            f"'authors' in the {DOCKSTORE_REGISTRY_CONF}.")

From 1310eb72d24bda774eb3b7a1593f0f4826ede7ec Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 13:07:03 +0200
Subject: [PATCH 13/28] new build_wf_lint_args to match what is happening with
 tools

---
 planemo/commands/cmd_workflow_lint.py | 10 +++++-----
 planemo/workflow_lint.py              |  7 +++++++
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 5cdf0c4e1..cb8b6adcb 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -4,9 +4,10 @@
 
 from planemo import options
 from planemo.cli import command_function
-from planemo.lint import build_lint_args
-from planemo.workflow_lint import lint_workflow_artifacts_on_paths
-
+from planemo.workflow_lint import (
+    build_wf_lint_args,
+    lint_workflow_artifacts_on_paths
+)
 
 @click.command("workflow_lint")
 @options.optional_tools_or_packages_arg(multiple=True)
@@ -24,8 +25,7 @@
 def cli(ctx, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
-    lint_args = build_lint_args(ctx, **kwds)
-    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
+    lint_args = build_wf_lint_args(ctx, **kwds)
     exit_code = lint_workflow_artifacts_on_paths(
         ctx,
         paths,
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 389457199..61b0a809b 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -39,6 +39,7 @@
     output_labels,
     required_input_labels,
 )
+from planemo.lint import build_lint_args
 from planemo.runnable import (
     cases,
     for_path,
@@ -59,6 +60,12 @@ class WorkflowLintContext(LintContext):
     training_topic = None
 
 
+def build_wf_lint_args(ctx, **kwds):
+    lint_args = build_lint_args(ctx, **kwds)
+    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
+    return lint_args
+
+
 def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
     workflows = []
     all_workflow_paths = list(find_workflow_descriptions(directory))

From 906c5cac6d8d5c595a09e10b52c97d55c028087c Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 15:35:33 +0200
Subject: [PATCH 14/28] fix error on CHANGELOG get version

---
 planemo/workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 61b0a809b..39812aeec 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -621,7 +621,7 @@ def _lint_release(path, lint_context):
         lint_context.error(f"The workflow {path} has no release")
     else:
         # Try to get the version from the CHANGELOG:
-        version = _get_changelog_version(os.path.join(os.path.dirname(path), "CHANGELOG.md"))
+        version = _get_changelog_version(os.path.dirname(path))
         if version != "" and workflow_dict.get("release") != version:
             lint_context.error(f"The release of workflow {path} does not match "
                                "the version in the CHANGELOG.")

From 39480a8664ba24207ada5e3d590f4e879e25a048 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 15:44:16 +0200
Subject: [PATCH 15/28] add tests

---
 .../.dockstore.yml                            | 11 +++
 .../basic_wf_iwc_invalid_version/CHANGELOG.md |  5 +
 .../basic_wf_iwc_invalid_version/README.md    |  3 +
 .../Super-simple-workflow-tests.yml           | 10 ++
 .../Super-simple-workflow.ga                  | 95 +++++++++++++++++++
 tests/test_cmd_workflow_lint.py               | 38 ++++++++
 6 files changed, 162 insertions(+)
 create mode 100644 tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml
 create mode 100644 tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md
 create mode 100644 tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md
 create mode 100644 tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml
 create mode 100644 tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga

diff --git a/tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml b/tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml
new file mode 100644
index 000000000..50c716fee
--- /dev/null
+++ b/tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml
@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Super-simple-workflow.ga
+  testParameterFiles:
+  - /Super-simple-workflow-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960
diff --git a/tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md b/tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md
new file mode 100644
index 000000000..7a859c1bf
--- /dev/null
+++ b/tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.1] 2024-06-17
+
+First release.
diff --git a/tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md b/tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md
new file mode 100644
index 000000000..a26db8ed6
--- /dev/null
+++ b/tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md
@@ -0,0 +1,3 @@
+# Super simple workflow
+
+This is a super simple workflow which generates a file with x lines with 'hello'
diff --git a/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml b/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml
new file mode 100644
index 000000000..9b1faff97
--- /dev/null
+++ b/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml
@@ -0,0 +1,10 @@
+- doc: Test outline for Super-simple-workflow
+  job:
+    n_rows: 5
+  outputs:
+    outfile:
+      asserts:
+        has_n_lines:
+          n: 5
+        has_line:
+          line: "hello"
diff --git a/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga b/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga
new file mode 100644
index 000000000..fcc756bd6
--- /dev/null
+++ b/tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga
@@ -0,0 +1,95 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This workflow generates a file with x lines with 'hello'",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0002-1964-4960",
+            "name": "Lucille Delisle"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "release": "0.2",
+    "name": "Super simple workflow",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Number of rows to generate",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Number of rows to generate",
+                    "name": "n_rows"
+                }
+            ],
+            "label": "n_rows",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "2ee42c13-83f5-4ac4-b35d-74294edf7dea",
+            "when": null
+        },
+        "1": {
+            "annotation": "this creates a file with a given number of lines",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "token_set_0|repeat_select|times": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "create file",
+            "name": "Create text file",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 236,
+                "top": 11
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "fbf99087e067",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"hello\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.3+galaxy1",
+            "type": "tool",
+            "uuid": "a86ff433-8dce-417c-baf0-bc106a93ee48",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "outfile",
+                    "output_name": "outfile",
+                    "uuid": "34572088-8ad8-4661-81a2-6dfe2d83a0fe"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "72c87042-27a8-4bcc-92af-ca74704e6161",
+    "version": 3
+}
\ No newline at end of file
diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index 02d38c2e7..d717dafdd 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -226,6 +226,44 @@ def test_workflow_linting_asserts(self):
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
         assert "ERROR: Invalid assertion in tests: assert_has_line missing a required argument: 'line'" in result.output
 
+    def test_workflow_linting_iwc(self):
+        # Check the output of workflow_lint --iwc on a basic workflow with .dockstore
+        repo = _wf_repo("basic_format2_dockstore")
+        lint_cmd = ["workflow_lint", "--skip", "best_practices", "--iwc", repo]
+        result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+        errors = [
+            "The file README.md is missing but required.",
+            "The file CHANGELOG.md is missing but required.",
+            ".dockstore.yml workflow entry missing recommended key name",
+            "Workflow  have no 'authors' in the .dockstore.yml.",
+            "The workflow tests/data/wf_repos/basic_format2_dockstore/basic_format2.gxwf.yml has no release"
+        ]
+
+        for error in errors:
+            assert error in result.output
+
+        # Check that skipping the good steps makes it work        
+        lint_cmd = ["workflow_lint", "--iwc", "--skip", "best_practices,required_files,dockstore_best_practices,release", repo]
+        self._check_exit_code(lint_cmd, exit_code=0)
+
+        # Check the output of workflow_lint --iwc on a good workflow but with an issue with the release
+        repo = _wf_repo("basic_wf_iwc_invalid_version")
+        lint_cmd = ["workflow_lint", "--iwc", repo]
+        result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+        errors = [
+            "The release of workflow",
+            " does not match the version in the CHANGELOG."
+        ]
+
+        for error in errors:
+            assert error in result.output
+
+        # Check that skipping the good steps makes it work        
+        lint_cmd = ["workflow_lint", "--iwc", "--skip", "release", repo]
+        self._check_exit_code(lint_cmd, exit_code=0)
+
 
 def _wf_repo(rel_path):
     return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)

From 7bb3a50b4b8732a397982d5243edb1d8f2a4675a Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 15:46:44 +0200
Subject: [PATCH 16/28] restore comma

---
 planemo/commands/cmd_workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index cb8b6adcb..dc94c03d7 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -29,6 +29,6 @@ def cli(ctx, paths, **kwds):
     exit_code = lint_workflow_artifacts_on_paths(
         ctx,
         paths,
-        lint_args
+        lint_args,
     )
     ctx.exit(exit_code)

From db8f24cc5eb9d9f3383b2071e94669a41abf50b9 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 15:49:11 +0200
Subject: [PATCH 17/28] test --iwc on file

---
 tests/test_cmd_workflow_lint.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index d717dafdd..be9615a7b 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -264,6 +264,17 @@ def test_workflow_linting_iwc(self):
         lint_cmd = ["workflow_lint", "--iwc", "--skip", "release", repo]
         self._check_exit_code(lint_cmd, exit_code=0)
 
+        # Check the output of workflow_lint --iwc on a file raise an error
+        repo = _wf_repo("wf1.ga")
+        lint_cmd = ["workflow_lint", "--iwc", repo]
+        result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+        errors = [
+            "ValueError: iwc standards can only be checked on directories."
+        ]
+
+        for error in errors:
+            assert error in result.output
 
 def _wf_repo(rel_path):
     return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)

From 22112e88f98da759c75bb9895007c2edf44da50b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 16:20:07 +0200
Subject: [PATCH 18/28] remove path from asserts output

---
 tests/test_cmd_workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index be9615a7b..1c872f525 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -237,7 +237,7 @@ def test_workflow_linting_iwc(self):
             "The file CHANGELOG.md is missing but required.",
             ".dockstore.yml workflow entry missing recommended key name",
             "Workflow  have no 'authors' in the .dockstore.yml.",
-            "The workflow tests/data/wf_repos/basic_format2_dockstore/basic_format2.gxwf.yml has no release"
+            "has no release"
         ]
 
         for error in errors:

From 147296ae1cb3e31e2139eb28aa2ae3e7fbfb6997 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 17:38:45 +0200
Subject: [PATCH 19/28] run black

---
 planemo/commands/cmd_workflow_lint.py |  6 +--
 planemo/workflow_lint.py              | 57 ++++++++++++++-------------
 tests/test_cmd_workflow_lint.py       | 24 +++++------
 3 files changed, 45 insertions(+), 42 deletions(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index dc94c03d7..2508c6236 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -4,10 +4,8 @@
 
 from planemo import options
 from planemo.cli import command_function
-from planemo.workflow_lint import (
-    build_wf_lint_args,
-    lint_workflow_artifacts_on_paths
-)
+from planemo.workflow_lint import build_wf_lint_args, lint_workflow_artifacts_on_paths
+
 
 @click.command("workflow_lint")
 @options.optional_tools_or_packages_arg(multiple=True)
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 39812aeec..190221277 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -156,7 +156,11 @@ def _lint_workflow_artifacts_on_path(
         if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:
             lint_context.lint("lint_dockstore", _lint_dockstore_config, potential_workflow_artifact_path)
             if iwc_grade:
-                lint_context.lint("lint_dockstore_best_practices", _lint_dockstore_config_best_practices, potential_workflow_artifact_path)
+                lint_context.lint(
+                    "lint_dockstore_best_practices",
+                    _lint_dockstore_config_best_practices,
+                    potential_workflow_artifact_path,
+                )
 
         elif looks_like_a_workflow(potential_workflow_artifact_path):
 
@@ -469,15 +473,16 @@ def _lint_dockstore_workflow_entry(
     # Check there is no space in name:
     workflow_name = workflow_entry.get("name", "")
     # Check the name has no space
-    if ' ' in workflow_name:
-        lint_context.error("Dockstore does not accept workflow names with space.",
-                           f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.")
+    if " " in workflow_name:
+        lint_context.error(
+            "Dockstore does not accept workflow names with space.",
+            f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.",
+        )
 
     # Check there is not mailto
-    for author in workflow_entry.get('authors', []):
-        if author.get('email', '').startswith('mailto:'):
-            lint_context.error("email field of the .dockstore.yml must not "
-                               "contain 'mailto:'")
+    for author in workflow_entry.get("authors", []):
+        if author.get("email", "").startswith("mailto:"):
+            lint_context.error("email field of the .dockstore.yml must not " "contain 'mailto:'")
 
 
 def looks_like_a_workflow(path: str) -> bool:
@@ -583,48 +588,47 @@ def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: T
 
 def _lint_required_files_workflow_dir(path: str, lint_context: WorkflowLintContext) -> None:
     # Check all required files are present
-    required_files = \
-        ['README.md', 'CHANGELOG.md', '.dockstore.yml']
+    required_files = ["README.md", "CHANGELOG.md", ".dockstore.yml"]
     for required_file in required_files:
         if not os.path.exists(os.path.join(path, required_file)):
-            lint_context.error(f"The file {required_file} is"
-                               " missing but required.")
+            lint_context.error(f"The file {required_file} is" " missing but required.")
 
 
 def _get_changelog_version(path: str) -> str:
     # Get the version from the CHANGELOG.md
     version = ""
-    if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
+    if not os.path.exists(os.path.join(path, "CHANGELOG.md")):
         return version
-    with open(os.path.join(path, 'CHANGELOG.md'), 'r') as f:
+    with open(os.path.join(path, "CHANGELOG.md"), "r") as f:
         for line in f:
-            if line.startswith('## ['):
-                version = line.split(']')[0].replace('## [', '')
+            if line.startswith("## ["):
+                version = line.split("]")[0].replace("## [", "")
                 break
     return version
 
 
 def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
     # Check the version can be get from the CHANGELOG.md
-    if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
+    if not os.path.exists(os.path.join(path, "CHANGELOG.md")):
         return
     if _get_changelog_version(path) == "":
-        lint_context.error("No version found in CHANGELOG. "
-                           "The version should be in a line that starts like "
-                           "'## [version number]'")
+        lint_context.error(
+            "No version found in CHANGELOG. "
+            "The version should be in a line that starts like "
+            "'## [version number]'"
+        )
 
 
 def _lint_release(path, lint_context):
     with open(path) as f:
         workflow_dict = ordered_load(f)
-    if 'release' not in workflow_dict:
+    if "release" not in workflow_dict:
         lint_context.error(f"The workflow {path} has no release")
     else:
         # Try to get the version from the CHANGELOG:
         version = _get_changelog_version(os.path.dirname(path))
         if version != "" and workflow_dict.get("release") != version:
-            lint_context.error(f"The release of workflow {path} does not match "
-                               "the version in the CHANGELOG.")
+            lint_context.error(f"The release of workflow {path} does not match " "the version in the CHANGELOG.")
 
 
 def _lint_dockstore_config_best_practices(path: str, lint_context: WorkflowLintContext) -> None:
@@ -634,7 +638,7 @@ def _lint_dockstore_config_best_practices(path: str, lint_context: WorkflowLintC
             dockstore_yaml = yaml.safe_load(f)
     except Exception:
         return
-    
+
     if not isinstance(dockstore_yaml, dict):
         return
 
@@ -655,6 +659,5 @@ def _lint_dockstore_workflow_entry_best_practices(
 
     workflow_name = workflow_entry.get("name", "")
     # Check there is at least one author
-    if len(workflow_entry.get('authors', [])) == 0:
-        lint_context.error(f"Workflow {workflow_name} have no "
-                            f"'authors' in the {DOCKSTORE_REGISTRY_CONF}.")
+    if len(workflow_entry.get("authors", [])) == 0:
+        lint_context.error(f"Workflow {workflow_name} have no 'authors' in the {DOCKSTORE_REGISTRY_CONF}.")
diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index 1c872f525..ea26e53a8 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -237,14 +237,20 @@ def test_workflow_linting_iwc(self):
             "The file CHANGELOG.md is missing but required.",
             ".dockstore.yml workflow entry missing recommended key name",
             "Workflow  have no 'authors' in the .dockstore.yml.",
-            "has no release"
+            "has no release",
         ]
 
         for error in errors:
             assert error in result.output
 
-        # Check that skipping the good steps makes it work        
-        lint_cmd = ["workflow_lint", "--iwc", "--skip", "best_practices,required_files,dockstore_best_practices,release", repo]
+        # Check that skipping the good steps makes it work
+        lint_cmd = [
+            "workflow_lint",
+            "--iwc",
+            "--skip",
+            "best_practices,required_files,dockstore_best_practices,release",
+            repo,
+        ]
         self._check_exit_code(lint_cmd, exit_code=0)
 
         # Check the output of workflow_lint --iwc on a good workflow but with an issue with the release
@@ -252,15 +258,12 @@ def test_workflow_linting_iwc(self):
         lint_cmd = ["workflow_lint", "--iwc", repo]
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
 
-        errors = [
-            "The release of workflow",
-            " does not match the version in the CHANGELOG."
-        ]
+        errors = ["The release of workflow", " does not match the version in the CHANGELOG."]
 
         for error in errors:
             assert error in result.output
 
-        # Check that skipping the good steps makes it work        
+        # Check that skipping the good steps makes it work
         lint_cmd = ["workflow_lint", "--iwc", "--skip", "release", repo]
         self._check_exit_code(lint_cmd, exit_code=0)
 
@@ -269,12 +272,11 @@ def test_workflow_linting_iwc(self):
         lint_cmd = ["workflow_lint", "--iwc", repo]
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
 
-        errors = [
-            "ValueError: iwc standards can only be checked on directories."
-        ]
+        errors = ["ValueError: iwc standards can only be checked on directories."]
 
         for error in errors:
             assert error in result.output
 
+
 def _wf_repo(rel_path):
     return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)

From f5af20fe79c3869a706686efa9344a5b8ed67eb2 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 17:45:15 +0200
Subject: [PATCH 20/28] run isort

---
 planemo/commands/cmd_workflow_lint.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 2508c6236..91bcacfa3 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -4,7 +4,10 @@
 
 from planemo import options
 from planemo.cli import command_function
-from planemo.workflow_lint import build_wf_lint_args, lint_workflow_artifacts_on_paths
+from planemo.workflow_lint import (
+    build_wf_lint_args,
+    lint_workflow_artifacts_on_paths,
+)
 
 
 @click.command("workflow_lint")

From 6e8f0ce67e278c6a0fff46f871bbfd9273cd6697 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 18:04:07 +0200
Subject: [PATCH 21/28] fix strange output when no --skip

---
 planemo/lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/planemo/lint.py b/planemo/lint.py
index 5b85022de..c5964428a 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -23,7 +23,7 @@ def build_lint_args(ctx, **kwds):
         skip = ctx.global_config.get("lint_skip", "")
         if isinstance(skip, list):
             skip = ",".join(skip)
-    skip_types = [s.strip() for s in skip.split(",")]
+    skip_types = [s.strip() for s in skip.split(",") if s.strip()]
 
     for skip_file in kwds.get("skip_file", []):
         with open(skip_file) as f:

From f748c11dfe9a1326772d7aabce948d0eee4dee16 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 18:14:38 +0200
Subject: [PATCH 22/28] fix final test

---
 tests/test_cmd_workflow_lint.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index ea26e53a8..2a5920bf8 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -271,11 +271,9 @@ def test_workflow_linting_iwc(self):
         repo = _wf_repo("wf1.ga")
         lint_cmd = ["workflow_lint", "--iwc", repo]
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
-
-        errors = ["ValueError: iwc standards can only be checked on directories."]
-
-        for error in errors:
-            assert error in result.output
+        assert result.exit_code == 1
+        assert isinstance(result.exception, ValueError)
+        assert str(result.exception) == "iwc standards can only be checked on directories."
 
 
 def _wf_repo(rel_path):

From 0d8dbd6c67f30a2248b18199b7a0c67d2246d6d3 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 22:50:41 +0200
Subject: [PATCH 23/28] change strategy for iwc on files

---
 planemo/workflow_lint.py        |  2 +-
 tests/test_cmd_workflow_lint.py | 39 ++++++++++++++-------------------
 2 files changed, 18 insertions(+), 23 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 190221277..0a2cbda04 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -148,7 +148,7 @@ def _lint_workflow_artifacts_on_path(
     iwc_grade = lint_args["iwc_grade"] == "True"
     if iwc_grade:
         if not os.path.isdir(path):
-            raise ValueError("iwc standards can only be checked on directories.")
+            path = os.path.dirname(path)
         lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
         lint_context.lint("lint_changelog", _lint_changelog_version, path)
 
diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index 2a5920bf8..c3155489e 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -228,20 +228,23 @@ def test_workflow_linting_asserts(self):
 
     def test_workflow_linting_iwc(self):
         # Check the output of workflow_lint --iwc on a basic workflow with .dockstore
-        repo = _wf_repo("basic_format2_dockstore")
-        lint_cmd = ["workflow_lint", "--skip", "best_practices", "--iwc", repo]
-        result = self._runner.invoke(self._cli.planemo, lint_cmd)
-
-        errors = [
-            "The file README.md is missing but required.",
-            "The file CHANGELOG.md is missing but required.",
-            ".dockstore.yml workflow entry missing recommended key name",
-            "Workflow  have no 'authors' in the .dockstore.yml.",
-            "has no release",
-        ]
-
-        for error in errors:
-            assert error in result.output
+        for repo in [
+            _wf_repo("basic_format2_dockstore"),
+            _wf_repo(os.path.join("basic_format2_dockstore", "basic_format2.gxwf.yml"))
+        ]:
+            lint_cmd = ["workflow_lint", "--skip", "best_practices", "--iwc", repo]
+            result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+            errors = [
+                "The file README.md is missing but required.",
+                "The file CHANGELOG.md is missing but required.",
+                ".dockstore.yml workflow entry missing recommended key name",
+                "Workflow  have no 'authors' in the .dockstore.yml.",
+                "has no release",
+            ]
+
+            for error in errors:
+                assert error in result.output
 
         # Check that skipping the good steps makes it work
         lint_cmd = [
@@ -267,14 +270,6 @@ def test_workflow_linting_iwc(self):
         lint_cmd = ["workflow_lint", "--iwc", "--skip", "release", repo]
         self._check_exit_code(lint_cmd, exit_code=0)
 
-        # Check the output of workflow_lint --iwc on a file raise an error
-        repo = _wf_repo("wf1.ga")
-        lint_cmd = ["workflow_lint", "--iwc", repo]
-        result = self._runner.invoke(self._cli.planemo, lint_cmd)
-        assert result.exit_code == 1
-        assert isinstance(result.exception, ValueError)
-        assert str(result.exception) == "iwc standards can only be checked on directories."
-
 
 def _wf_repo(rel_path):
     return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)

From 64f90768bb243a37feb4b3bce5f235af078cd6e6 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 1 Jul 2024 23:04:58 +0200
Subject: [PATCH 24/28] add comma

---
 tests/test_cmd_workflow_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index c3155489e..9377464f5 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -230,7 +230,7 @@ def test_workflow_linting_iwc(self):
         # Check the output of workflow_lint --iwc on a basic workflow with .dockstore
         for repo in [
             _wf_repo("basic_format2_dockstore"),
-            _wf_repo(os.path.join("basic_format2_dockstore", "basic_format2.gxwf.yml"))
+            _wf_repo(os.path.join("basic_format2_dockstore", "basic_format2.gxwf.yml")),
         ]:
             lint_cmd = ["workflow_lint", "--skip", "best_practices", "--iwc", repo]
             result = self._runner.invoke(self._cli.planemo, lint_cmd)

From bafecffb2f1e89a0bb8dd309481495dce305bed3 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 2 Jul 2024 12:15:32 +0100
Subject: [PATCH 25/28] Add type annotation

---
 planemo/commands/cmd_lint.py          |  7 +++++--
 planemo/commands/cmd_shed_lint.py     |  7 +++++--
 planemo/commands/cmd_workflow_lint.py |  7 +++++--
 planemo/lint.py                       | 12 ++++++++++--
 planemo/shed_lint.py                  |  6 +++++-
 planemo/tool_lint.py                  |  6 +++++-
 planemo/workflow_lint.py              |  4 ++--
 7 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/planemo/commands/cmd_lint.py b/planemo/commands/cmd_lint.py
index 85a3c77cc..f6ca5a454 100644
--- a/planemo/commands/cmd_lint.py
+++ b/planemo/commands/cmd_lint.py
@@ -3,7 +3,10 @@
 import click
 
 from planemo import options
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 from planemo.tool_lint import (
     build_tool_lint_args,
     lint_tools_on_path,
@@ -43,7 +46,7 @@
 # default=False,
 # )
 @command_function
-def cli(ctx, uris, **kwds):
+def cli(ctx: PlanemoCliContext, uris, **kwds):
     """Check for common errors and best practices."""
     lint_args = build_tool_lint_args(ctx, **kwds)
     exit_code = lint_tools_on_path(ctx, uris, lint_args, recursive=kwds["recursive"])
diff --git a/planemo/commands/cmd_shed_lint.py b/planemo/commands/cmd_shed_lint.py
index 80f420b31..70bb5c9d4 100644
--- a/planemo/commands/cmd_shed_lint.py
+++ b/planemo/commands/cmd_shed_lint.py
@@ -7,7 +7,10 @@
     shed,
     shed_lint,
 )
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 
 
 @click.command("shed_lint")
@@ -41,7 +44,7 @@
 #     default=False,
 # )
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx: PlanemoCliContext, paths, **kwds):
     """Check Tool Shed repository for common issues.
 
     With the ``--tools`` flag, this command lints actual Galaxy tools
diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 91bcacfa3..e71fdd61f 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -3,7 +3,10 @@
 import click
 
 from planemo import options
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 from planemo.workflow_lint import (
     build_wf_lint_args,
     lint_workflow_artifacts_on_paths,
@@ -23,7 +26,7 @@
     help="Check workflows directory with the standards of iwc",
 )
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx: PlanemoCliContext, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
     lint_args = build_wf_lint_args(ctx, **kwds)
diff --git a/planemo/lint.py b/planemo/lint.py
index c14247e7a..87bfd5aaa 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -1,6 +1,11 @@
 """Utilities to help linting various targets."""
 
 import os
+from typing import (
+    Any,
+    Dict,
+    TYPE_CHECKING,
+)
 from urllib.request import urlopen
 
 import requests
@@ -13,8 +18,11 @@
 from planemo.shed import find_urls_for_xml
 from planemo.xml import validation
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 
-def build_lint_args(ctx, **kwds):
+def build_lint_args(ctx: "PlanemoCliContext", **kwds) -> Dict[str, Any]:
     """Handle common report, error, and skip linting arguments."""
     report_level = kwds.get("report_level", "all")
     fail_level = kwds.get("fail_level", "warn")
@@ -39,7 +47,7 @@ def build_lint_args(ctx, **kwds):
     if len(invalid_skip_types):
         error(f"Unknown linter type(s) {invalid_skip_types} in list of linters to be skipped. Known linters {linters}")
 
-    lint_args = dict(
+    lint_args: Dict[str, Any] = dict(
         level=report_level,
         fail_level=fail_level,
         skip_types=skip_types,
diff --git a/planemo/shed_lint.py b/planemo/shed_lint.py
index 322d16756..b3d03760b 100644
--- a/planemo/shed_lint.py
+++ b/planemo/shed_lint.py
@@ -2,6 +2,7 @@
 
 import os
 import xml.etree.ElementTree as ET
+from typing import TYPE_CHECKING
 
 import yaml
 from galaxy.tool_util.lint import lint_tool_source_with
@@ -31,6 +32,9 @@
 from planemo.tools import yield_tool_sources
 from planemo.xml import XSDS_PATH
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 TOOL_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "tool_dependencies.xsd")
 REPO_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "repository_dependencies.xsd")
 
@@ -50,7 +54,7 @@
 ]
 
 
-def lint_repository(ctx, realized_repository, **kwds):
+def lint_repository(ctx: "PlanemoCliContext", realized_repository, **kwds):
     """Lint a realized shed repository.
 
     See :mod:`planemo.shed` for details on constructing a realized
diff --git a/planemo/tool_lint.py b/planemo/tool_lint.py
index 9e72d2646..d6ccd509e 100644
--- a/planemo/tool_lint.py
+++ b/planemo/tool_lint.py
@@ -1,4 +1,5 @@
 from os.path import basename
+from typing import TYPE_CHECKING
 
 from galaxy.tool_util.lint import lint_tool_source
 
@@ -22,10 +23,13 @@
     yield_tool_sources_on_paths,
 )
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 LINTING_TOOL_MESSAGE = "Linting tool %s"
 
 
-def build_tool_lint_args(ctx, **kwds):
+def build_tool_lint_args(ctx: "PlanemoCliContext", **kwds):
     lint_args = build_lint_args(ctx, **kwds)
     extra_modules = _lint_extra_modules(**kwds)
     lint_args["extra_modules"] = extra_modules
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 0a2cbda04..b79c8ca4b 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -60,9 +60,9 @@ class WorkflowLintContext(LintContext):
     training_topic = None
 
 
-def build_wf_lint_args(ctx, **kwds):
+def build_wf_lint_args(ctx: "PlanemoCliContext", **kwds) -> Dict[str, Any]:
     lint_args = build_lint_args(ctx, **kwds)
-    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
+    lint_args["iwc_grade"] = kwds.get("iwc", False)
     return lint_args
 
 

From b1eedf4ef70fab31d28a8280edab4a1eaa28e6ca Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 2 Jul 2024 13:21:22 +0200
Subject: [PATCH 26/28] Apply suggestions from @bernt-matthias

Co-authored-by: M Bernt <m.bernt@ufz.de>
---
 planemo/workflow_lint.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index b79c8ca4b..c1f9df8c8 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -145,8 +145,7 @@ def lint_workflow_artifacts_on_paths(
 def _lint_workflow_artifacts_on_path(
     lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
 ) -> None:
-    iwc_grade = lint_args["iwc_grade"] == "True"
-    if iwc_grade:
+    if lint_args["iwc_grade"]:
         if not os.path.isdir(path):
             path = os.path.dirname(path)
         lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
@@ -155,7 +154,7 @@ def _lint_workflow_artifacts_on_path(
     for potential_workflow_artifact_path in find_potential_workflow_files(path):
         if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:
             lint_context.lint("lint_dockstore", _lint_dockstore_config, potential_workflow_artifact_path)
-            if iwc_grade:
+            if lint_args["iwc_grade"]:
                 lint_context.lint(
                     "lint_dockstore_best_practices",
                     _lint_dockstore_config_best_practices,
@@ -172,7 +171,7 @@ def structure(path, lint_context):
                 lint_func(lint_context, workflow_dict, path=path)
 
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
-            if iwc_grade:
+            if lint_args["iwc_grade"]:
                 lint_context.lint("lint_release", _lint_release, potential_workflow_artifact_path)
             lint_context.lint("lint_best_practices", _lint_best_practices, potential_workflow_artifact_path)
             lint_context.lint("lint_tests", _lint_tsts, potential_workflow_artifact_path)

From ecdcf0f80c473a4e8ca5748470151ee7c68a5199 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 2 Jul 2024 13:30:22 +0200
Subject: [PATCH 27/28] fix lint_args typing to different places

---
 planemo/tool_lint.py     | 8 ++++++--
 planemo/workflow_lint.py | 4 ++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/planemo/tool_lint.py b/planemo/tool_lint.py
index d6ccd509e..eea2ad7ff 100644
--- a/planemo/tool_lint.py
+++ b/planemo/tool_lint.py
@@ -1,5 +1,9 @@
 from os.path import basename
-from typing import TYPE_CHECKING
+from typing import (
+    Any,
+    Dict,
+    TYPE_CHECKING,
+)
 
 from galaxy.tool_util.lint import lint_tool_source
 
@@ -29,7 +33,7 @@
 LINTING_TOOL_MESSAGE = "Linting tool %s"
 
 
-def build_tool_lint_args(ctx: "PlanemoCliContext", **kwds):
+def build_tool_lint_args(ctx: "PlanemoCliContext", **kwds) -> Dict[str, Any]:
     lint_args = build_lint_args(ctx, **kwds)
     extra_modules = _lint_extra_modules(**kwds)
     lint_args["extra_modules"] = extra_modules
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index c1f9df8c8..085a25fd7 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -129,7 +129,7 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
 
 
 def lint_workflow_artifacts_on_paths(
-    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]
+    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Any]
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
@@ -143,7 +143,7 @@ def lint_workflow_artifacts_on_paths(
 
 
 def _lint_workflow_artifacts_on_path(
-    lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
+    lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Any]
 ) -> None:
     if lint_args["iwc_grade"]:
         if not os.path.isdir(path):

From 2f7c139cb0cc6e9984bf6b0c29dcd950da2ad5f7 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 2 Jul 2024 13:35:02 +0200
Subject: [PATCH 28/28] remove unused Union

---
 planemo/workflow_lint.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
index 085a25fd7..b8403f41c 100644
--- a/planemo/workflow_lint.py
+++ b/planemo/workflow_lint.py
@@ -12,7 +12,6 @@
     Optional,
     Tuple,
     TYPE_CHECKING,
-    Union,
 )
 
 import requests
@@ -128,9 +127,7 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
     return contents
 
 
-def lint_workflow_artifacts_on_paths(
-    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Any]
-) -> int:
+def lint_workflow_artifacts_on_paths(ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Any]) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
     for path in paths:
@@ -142,9 +139,7 @@ def lint_workflow_artifacts_on_paths(
         return EXIT_CODE_OK
 
 
-def _lint_workflow_artifacts_on_path(
-    lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Any]
-) -> None:
+def _lint_workflow_artifacts_on_path(lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Any]) -> None:
     if lint_args["iwc_grade"]:
         if not os.path.isdir(path):
             path = os.path.dirname(path)