Fix git packager for git repo with submodules (#109)

src/nemo_run/core/packaging/git.py

@@ -57,6 +57,9 @@ class GitArchivePackager(Packager):
     #: Can be a branch name or a commit ref like HEAD.
     ref: str = "HEAD"
 
+    #: Include submodules in the archive.
+    include_submodules: bool = True
+
     #: Include extra files in the archive which matches include_pattern
     #: This str will be included in the command as: find {include_pattern} -type f to get the list of extra files to include in the archive
     include_pattern: str = ""
@@ -109,40 +112,42 @@ def package(self, path: Path, job_dir: str, name: str) -> str:
             ), "Your repo has untracked files. Please track your files via git or set check_untracked_files to False to proceed with packaging."
 
         ctx = Context()
+        # we first add git files into an uncompressed archive
+        # then we add submodule files into that archive
+        # then we add an extra files from pattern to that archive
+        # finally we compress it (cannot compress right away, since adding files is not possible)
+        git_archive_cmd = (
+            f"git archive --format=tar --output={output_file}.tmp {self.ref}:{git_sub_path}"
+        )
+        git_submodule_cmd = f"""git submodule foreach --recursive \
+'git archive --format=tar --prefix=$sm_path/ --output=$sha1.tmp HEAD && tar -Af {output_file}.tmp $sha1.tmp && rm $sha1.tmp'"""
+        with ctx.cd(git_base_path):
+            ctx.run(git_archive_cmd)
+            if self.include_submodules:
+                ctx.run(git_submodule_cmd)
+
         if self.include_pattern:
             include_pattern_relative_path = self.include_pattern_relative_path or shlex.quote(
                 str(git_base_path)
             )
             relative_include_pattern = os.path.relpath(
                 self.include_pattern, include_pattern_relative_path
             )
-            # we first add git files into an uncompressed archive
-            # then we add an extra files from pattern to that archive
-            # finally we compress it (cannot compress right away, since adding files is not possible)
-            git_archive_cmd = (
-                f"git archive --format=tar --output={output_file}.tmp {self.ref}:{git_sub_path}"
-            )
             include_pattern_cmd = f"find {relative_include_pattern} -type f | tar -cf {os.path.join(git_base_path, 'additional.tmp')} -T -"
-            tar_concatenate_cmd = f"tar -Af {output_file}.tmp additional.tmp"
-            gzip_cmd = f"gzip -c {output_file}.tmp > {output_file}"
-            rm_cmd = f"rm {output_file}.tmp additional.tmp"
-
-            with ctx.cd(git_base_path):
-                ctx.run(git_archive_cmd)
+            tar_concatenate_cmd = f"tar -Af {output_file}.tmp additional.tmp && rm additional.tmp"
 
             with ctx.cd(include_pattern_relative_path):
                 ctx.run(include_pattern_cmd)
 
             with ctx.cd(git_base_path):
                 ctx.run(tar_concatenate_cmd)
-                ctx.run(gzip_cmd)
-                ctx.run(rm_cmd)
-        else:
-            with ctx.cd(git_base_path):
-                git_archive_cmd = (
-                    f"git archive --format=tar.gz --output={output_file} {self.ref}:{git_sub_path}"
-                )
-                ctx.run(git_archive_cmd)
+
+        gzip_cmd = f"gzip -c {output_file}.tmp > {output_file}"
+        rm_cmd = f"rm {output_file}.tmp"
+
+        with ctx.cd(git_base_path):
+            ctx.run(gzip_cmd)
+            ctx.run(rm_cmd)
 
         return output_file
 

test/core/packaging/test_git.py

@@ -290,3 +290,60 @@ def test_untracked_files_raises_exception(temp_repo):
         f.write("Untracked file")
     with pytest.raises(AssertionError, match="Your repo has untracked files"):
         packager.package(temp_repo, str(temp_repo), "test")
+
+
+@patch("nemo_run.core.packaging.git.Context", MockContext)
+def test_package_with_include_submodules(packager, temp_repo):
+    temp_repo = Path(temp_repo)
+    # Create a submodule
+    submodule_path = temp_repo / "submodule"
+    submodule_path.mkdir()
+    os.chdir(str(submodule_path))
+    subprocess.check_call(["git", "init", "--initial-branch=main"])
+    open("submodule_file.txt", "w").write("Submodule file")
+    subprocess.check_call(["git", "add", "."])
+    subprocess.check_call(["git", "commit", "-m", "Initial submodule commit"])
+    os.chdir(str(temp_repo))
+    subprocess.check_call(["git", "submodule", "add", str(submodule_path)])
+    subprocess.check_call(["git", "commit", "-m", "Add submodule"])
+
+    packager = GitArchivePackager(ref="HEAD", include_submodules=True)
+    with tempfile.TemporaryDirectory() as job_dir:
+        output_file = packager.package(Path(temp_repo), job_dir, "test_package")
+        assert os.path.exists(output_file)
+        subprocess.check_call(shlex.split(f"mkdir -p {os.path.join(job_dir, 'extracted_output')}"))
+        subprocess.check_call(
+            shlex.split(f"tar -xvzf {output_file} -C {os.path.join(job_dir, 'extracted_output')}"),
+        )
+        cmp = filecmp.dircmp(
+            os.path.join(temp_repo, "submodule"),
+            os.path.join(job_dir, "extracted_output", "submodule"),
+        )
+        assert cmp.left_list == cmp.right_list
+        assert not cmp.diff_files
+
+
+@patch("nemo_run.core.packaging.git.Context", MockContext)
+def test_package_without_include_submodules(packager, temp_repo):
+    temp_repo = Path(temp_repo)
+    # Create a submodule
+    submodule_path = temp_repo / "submodule"
+    submodule_path.mkdir()
+    os.chdir(str(submodule_path))
+    subprocess.check_call(["git", "init", "--initial-branch=main"])
+    open("submodule_file.txt", "w").write("Submodule file")
+    subprocess.check_call(["git", "add", "."])
+    subprocess.check_call(["git", "commit", "-m", "Initial submodule commit"])
+    os.chdir(str(temp_repo))
+    subprocess.check_call(["git", "submodule", "add", str(submodule_path)])
+    subprocess.check_call(["git", "commit", "-m", "Add submodule"])
+
+    packager = GitArchivePackager(ref="HEAD", include_submodules=False)
+    with tempfile.TemporaryDirectory() as job_dir:
+        output_file = packager.package(Path(temp_repo), job_dir, "test_package")
+        assert os.path.exists(output_file)
+        subprocess.check_call(shlex.split(f"mkdir -p {os.path.join(job_dir, 'extracted_output')}"))
+        subprocess.check_call(
+            shlex.split(f"tar -xvzf {output_file} -C {os.path.join(job_dir, 'extracted_output')}"),
+        )
+        assert len(os.listdir(os.path.join(job_dir, "extracted_output", "submodule"))) == 0