oist · milesAraya · Aug 12, 2025 · Jun 16, 2025 · Jun 16, 2025 · Jun 17, 2025
diff --git a/.github/ISSUE_TEMPLATE/bug_report_en.md → .github/ISSUE_TEMPLATE/01_bug_report_en.md b/.github/ISSUE_TEMPLATE/bug_report_en.md → .github/ISSUE_TEMPLATE/01_bug_report_en.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request_en.md → ...b/ISSUE_TEMPLATE/11_feature_request_en.md b/.github/ISSUE_TEMPLATE/feature_request_en.md → ...b/ISSUE_TEMPLATE/11_feature_request_en.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report_jp.md b/.github/ISSUE_TEMPLATE/bug_report_jp.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request_jp.md → ...ub/ISSUE_TEMPLATE/developer_01_feature.md b/.github/ISSUE_TEMPLATE/feature_request_jp.md → ...ub/ISSUE_TEMPLATE/developer_01_feature.md
@@ -1,5 +1,5 @@
 ---
-name: Additional Feature
+name: (developer) Additional Feature
 about: Issue for Additional Feature
 title: ''
 labels: 'enhancement'
@@ -8,10 +8,13 @@ assignees: ''
 ---
 
 ### Overview
+
 > *Describes an overview of the feature
 
 ### References
+
 > *Links to design documentation and reference information
 
 ### Others
+
 > *Other comments etc.
diff --git a/.github/ISSUE_TEMPLATE/problem.md → ...ub/ISSUE_TEMPLATE/developer_02_problem.md b/.github/ISSUE_TEMPLATE/problem.md → ...ub/ISSUE_TEMPLATE/developer_02_problem.md
@@ -1,5 +1,5 @@
 ---
-name: Problem
+name: (developer) Problem
 about: Issue for Problem
 title: ''
 labels: ''
@@ -8,10 +8,13 @@ assignees: ''
 ---
 
 ### Problem
+
 > *Describes a summary of the problem
 
 ### Measures
+
 > *Describes expected measures
 
 ### Others
+
 > *Other comments etc.
diff --git a/.github/ISSUE_TEMPLATE/task.md → .github/ISSUE_TEMPLATE/developer_03_task.md b/.github/ISSUE_TEMPLATE/task.md → .github/ISSUE_TEMPLATE/developer_03_task.md
@@ -1,5 +1,5 @@
 ---
-name: Task
+name: (developer) Task
 about: Issue for Task
 title: ''
 labels: ''
@@ -8,13 +8,17 @@ assignees: ''
 ---
 
 ### Summary
+
 > *Describes a summary of the task
 
 ### Tasks
+
 > *Describes expected tasks
 
 ### References
+
 > *Links to reference information
 
 ### Others
+
 > *Other comments etc.
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,11 +1,15 @@
 ### Content
+
 > *Describes a content of the pull request
 
 ### References
+
 > *Links to reference information
 
 ### Testcase
+
 > *Testcase of the pull request
 
 ### Others
+
 > *Other comments etc.
diff --git a/codemeta.json b/codemeta.json
@@ -133,7 +133,7 @@
         "Docker",
         "Python 3.9"
     ],
-    "version": "2.2.0",
+    "version": "2.2.2",
     "developmentStatus": "active",
     "funding": "Brain/MINDS",
     "issueTracker": "https://github.com/oist/optinist/issues",

diff --git a/docs/conf.py b/docs/conf.py
@@ -19,7 +19,7 @@
 project = "OptiNiSt"
 copyright = f"{datetime.today().year}, OIST"
 author = ""
-release = "2.2.1"
+release = "2.2.2"
 
 # -- readthedocs -------------------------------------------------------------
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"

diff --git a/docs/specifications/architecture.md b/docs/specifications/architecture.md
@@ -27,7 +27,7 @@ Following is the summary of directory structure.
   - `.env`: Application environment variable definition file
     - Depending on usage, the following .env files are available
       - `.env`: Loads for all environments
-      - `.env.development`: Used during development (yarn start) 
+      - `.env.development`: Used during development (yarn start)
       - `.env.production`: Used during production builds (yarn build)
     - [Learn more](https://create-react-app.dev/docs/adding-custom-environment-variables/#what-other-env-files-can-be-used)
 

diff --git a/docs/specifications/data_nodes.md b/docs/specifications/data_nodes.md
@@ -21,10 +21,10 @@ OptiNiSt accepts a variety of data types. Data are added in "nodes", depending o
   - Can be transposed if specified in parameters
 - File Extension: ".csv"
 #### HDF5 / [NWB](https://nwb-schema.readthedocs.io/en/latest/format_description.html)
-- Format: Contains Groups, Datasets, Attributes (metadata). 
+- Format: Contains Groups, Datasets, Attributes (metadata).
   - A Group is similar to a folder and may contain an arbitrary number of other groups and datasets,
   - A Dataset describes an n-dimensional array and provides the primary means for storing data,
-  - An Attribute* is a small dataset that is attached to a specific group or dataset and is typically used to store metadata specific to the object they are associated with. 
+  - An Attribute* is a small dataset that is attached to a specific group or dataset and is typically used to store metadata specific to the object they are associated with.
  - ".hdf5", ".nwb", ".HDF5", ".NWB"
 #### Matlab
  - Format:
@@ -89,7 +89,7 @@ Defined in bar.py
 Expects 1D or 2D numpy array
 If 1D, converts to 2D with shape (1, length)
 
-    LineData:  
+    LineData:
 Defined in line.py
 Expects 2D numpy array
 
@@ -104,4 +104,4 @@ Expects 2D numpy array
 
     HTMLData:
 Defined in html.py
-Expects string HTML content -->
+Expects string HTML content -->
diff --git a/frontend/package.json b/frontend/package.json
@@ -1,6 +1,6 @@
 {
   "name": "optinist",
-  "version": "2.2.1",
+  "version": "2.2.2",
   "engines": {
     "node": ">=20.0.0"
   },

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "optinist"
 description = "Calcium Imaging Pipeline Tool"
-version = "2.2.1"
+version = "2.2.2"
 license = "GPL-3.0"
 authors = ["OIST <email@example.com>"]
 readme = "README.md"

diff --git a/run_cluster.py b/run_cluster.py
@@ -6,6 +6,8 @@
 
 from snakemake import snakemake
 
+from studio.app.common.core.experiment.experiment import ExptOutputPathIds
+from studio.app.common.core.utils.config_handler import ConfigReader
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.dir_path import DIRPATH
 
@@ -18,6 +20,7 @@ def main(args):
         print(f"Temporary work directory created at: {temp_workdir}")
 
         config_file_path = None
+        temp_config_file_path = None
 
         if args.config is None:
             raise FileNotFoundError(
@@ -34,12 +37,17 @@ def main(args):
             if not Path(config_file_path).exists():
                 raise FileNotFoundError(f"Config file not found: {args.config}")
 
-            shutil.copyfile(
-                config_file_path,
-                join_filepath([str(temp_workdir), str(Path(config_file_path).name)]),
+            temp_config_file_path = join_filepath(
+                [str(temp_workdir), Path(config_file_path).name]
             )
-            print(f"Config file copied from {config_file_path} to {temp_workdir}")
 
+            shutil.copyfile(config_file_path, temp_config_file_path)
+
+            print(
+                f"Config file copied from {config_file_path} to {temp_config_file_path}"
+            )
+
+        # Main snakemake execution
         snakemake_args = {
             "snakefile": DIRPATH.SNAKEMAKE_FILEPATH,
             "forceall": args.forceall,
@@ -49,19 +57,69 @@ def main(args):
         }
 
         if config_file_path is not None:
-            snakemake_args["configfiles"] = [str(config_file_path)]
+            snakemake_args["configfiles"] = [str(temp_config_file_path)]
 
         if args.use_conda:
             snakemake_args["conda_prefix"] = DIRPATH.SNAKEMAKE_CONDA_ENV_DIR
 
         print(f"Snakemake arguments: {snakemake_args}")
 
-        result = snakemake(**snakemake_args)
+        try:
+            result = snakemake(**snakemake_args)
+
+            if result:
+                print("snakemake execution succeeded.")
+                # Copy config file back to output directory for future reference
+                try:
+                    # Find the output directory from the last_output in config
+                    config_data = ConfigReader.read(config_file_path)
+                    if config_data and "last_output" in config_data:
+                        # Extract the last output path
+                        last_output_path = config_data["last_output"][0]
+                        # Construct absolute path and extract directory
+                        absolute_output_path = join_filepath(
+                            [DIRPATH.OUTPUT_DIR, last_output_path]
+                        )
+                        # Extract the workspace_id and unique_id
+                        path_ids = ExptOutputPathIds(
+                            os.path.dirname(absolute_output_path)
+                        )
+
+                        # Create the output directory path to copy the config file
+                        output_config_dir = join_filepath(
+                            [
+                                DIRPATH.OUTPUT_DIR,
+                                path_ids.workspace_id,
+                                path_ids.unique_id,
+                            ]
+                        )
+                        os.makedirs(output_config_dir, exist_ok=True)
+                        output_config_path = join_filepath(
+                            [output_config_dir, DIRPATH.SNAKEMAKE_CONFIG_YML]
+                        )
+
+                        shutil.copyfile(config_file_path, output_config_path)
+                        print(
+                            f"Config copied to output directory: {output_config_path}"
+                        )
+                    else:
+                        print(
+                            "Warning: No output path found in config, "
+                            "skipping config copy"
+                        )
+                except Exception as e:
+                    print(f"Warning: Failed to copy config to output directory: {e}")
+            else:
+                print("snakemake execution failed.")
+                print("Check for errors above in the snakemake output.")
 
-        if result:
-            print("snakemake execution succeeded.")
-        else:
-            print("snakemake execution failed.")
+        except Exception as e:
+            print(f"snakemake execution failed with exception: {e}")
+            import traceback
+
+            print("Full traceback:")
+            traceback.print_exc()
+            result = False
 
         return result
 

diff --git a/studio/app/common/core/rules/data.py b/studio/app/common/core/rules/data.py
@@ -27,7 +27,7 @@ def main():
 
         rule_config = RuleConfigReader.read(snakemake.params.name)
 
-        rule_config = SmkUtils.resolve_nwbfile_reference(rule_config)
+        rule_config = SmkUtils.resolve_nwbfile_reference(rule_config, snakemake.config)
 
         if NodeTypeUtil.check_nodetype_from_filetype(rule_config.type) == NodeType.DATA:
             if rule_config.type in [FILETYPE.IMAGE]:

diff --git a/studio/app/common/core/rules/func.py b/studio/app/common/core/rules/func.py
@@ -17,6 +17,7 @@
 def main():
     try:
         from studio.app.common.core.rules.runner import Runner
+        from studio.app.common.core.snakemake.smk_utils import SmkUtils
         from studio.app.common.core.snakemake.snakemake_reader import RuleConfigReader
         from studio.app.common.core.utils.filepath_creater import join_filepath
         from studio.app.dir_path import DIRPATH
@@ -28,6 +29,8 @@ def main():
 
         rule_config = RuleConfigReader.read(snakemake.params.name)
 
+        rule_config = SmkUtils.resolve_nwbfile_reference(rule_config, snakemake.config)
+
         rule_config.input = snakemake.input
         rule_config.output = snakemake.output[0]
         run_script_path = sys.argv[0]