From e5716819de7d959377ad29b048a686a156066475 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Jun 2023 15:49:29 +0200
Subject: [PATCH 1/3] add docs to commit new files before pytest

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index dacb50ebc4..5d5791c109 100644
--- a/README.md
+++ b/README.md
@@ -941,6 +941,8 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
+
 You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX
@@ -1199,6 +1201,8 @@ extra_env:
 
 To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+
 You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX

From 202ee4e9ba756fcae4fe3df1d4d0d9236b6f68a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 12 Jun 2023 14:32:43 +0000
Subject: [PATCH 2/3] check for uncommitted changes

---
 nf_core/components/components_test.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index c2b9abf569..b8a0d724c1 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -7,6 +7,7 @@
 import pytest
 import questionary
 import rich
+from git import Repo
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -179,6 +180,11 @@ def _run_pytests(self):
         console = rich.console.Console()
         console.rule(self.component_name, style="black")
 
+        # Check uncommitted changed
+        repo = Repo(self.dir)
+        if repo.is_dirty():
+            log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+
         # Set pytest arguments
         tag = self.component_name
         if self.component_type == "subworkflows":

From b4e8f823428eec9701e5496d06130ee0af72199e Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Jun 2023 16:01:08 +0200
Subject: [PATCH 3/3] catch InvalidGitRepositoryError

---
 nf_core/components/components_test.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index b8a0d724c1..37e275aea8 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -7,7 +7,7 @@
 import pytest
 import questionary
 import rich
-from git import Repo
+from git import InvalidGitRepositoryError, Repo
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -181,9 +181,12 @@ def _run_pytests(self):
         console.rule(self.component_name, style="black")
 
         # Check uncommitted changed
-        repo = Repo(self.dir)
-        if repo.is_dirty():
-            log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+        try:
+            repo = Repo(self.dir)
+            if repo.is_dirty():
+                log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+        except InvalidGitRepositoryError:
+            pass
 
         # Set pytest arguments
         tag = self.component_name