Revert commits after 5708459

Author: JoeZiminski

.github/workflows/code_test_and_deploy.yml

@@ -7,7 +7,7 @@ on:
     tags:
       - 'v*'
   pull_request:
-
+    types: [opened, synchronize, reopened, ready_for_review]
   schedule:
     # Cron runs on the 1st and 15th of every month.
     # This will only run on main by default.
@@ -20,7 +20,6 @@ jobs:
       - uses: neuroinformatics-unit/actions/lint@v2
 
   test:
-    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     needs: [linting]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
@@ -113,7 +112,7 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v6
+    - uses: actions/download-artifact@v5
       with:
         name: artifact
         path: dist

.pre-commit-config.yaml

@@ -31,12 +31,12 @@ repos:
         - id: rst-directive-colons
         - id: rst-inline-touching-normal
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.14.3
+      rev: v0.12.11
       hooks:
         - id: ruff
         - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.18.2
+      rev: v1.17.1
       hooks:
           - id: mypy
             additional_dependencies:

datashuttle/configs/canonical_configs.py

@@ -292,9 +292,9 @@ def get_tui_config_defaults() -> Dict:
     return settings
 
 
-def get_validation_templates_defaults() -> Dict:
-    """Return the default values for validation_templates."""
-    return {"validation_templates": {"on": False, "sub": None, "ses": None}}
+def get_name_templates_defaults() -> Dict:
+    """Return the default values for name_templates."""
+    return {"name_templates": {"on": False, "sub": None, "ses": None}}
 
 
 def get_persistent_settings_defaults() -> Dict:
@@ -306,7 +306,7 @@ def get_persistent_settings_defaults() -> Dict:
     """
     settings = {}
     settings.update(get_tui_config_defaults())
-    settings.update(get_validation_templates_defaults())
+    settings.update(get_name_templates_defaults())
 
     return settings
 

datashuttle/configs/config_class.py

@@ -62,6 +62,7 @@ def __init__(
 
         self.logging_path: Path
         self.hostkeys_path: Path
+        self.ssh_key_path: Path
         self.project_metadata_path: Path
 
     def setup_after_load(self) -> None:
@@ -299,6 +300,8 @@ def init_paths(self) -> None:
             self.project_name
         )
 
+        self.ssh_key_path = datashuttle_path / f"{self.project_name}_ssh_key"
+
         self.hostkeys_path = datashuttle_path / "hostkeys"
 
         self.logging_path = self.make_and_get_logging_path()

datashuttle/datashuttle_class.py

@@ -28,6 +28,7 @@
         TopLevelFolder,
     )
 
+import paramiko
 import yaml
 
 from datashuttle.configs import (
@@ -217,13 +218,13 @@ def create_folders(
         utils.log("\nFormatting Names...")
         ds_logger.log_names(["sub_names", "ses_names"], [sub_names, ses_names])
 
-        validation_templates = self.get_validation_templates()
+        name_templates = self.get_name_templates()
 
         format_sub, format_ses = self._format_and_validate_names(
             top_level_folder,
             sub_names,
             ses_names,
-            validation_templates,
+            name_templates,
             bypass_validation,
             allow_letters_in_sub_ses_values,
             log=True,
@@ -260,7 +261,7 @@ def _format_and_validate_names(
         top_level_folder: TopLevelFolder,
         sub_names: Union[str, List[str]],
         ses_names: Optional[Union[str, List[str]]],
-        validation_templates: Dict,
+        name_templates: Dict,
         bypass_validation: bool,
         allow_letters_in_sub_ses_values: bool,
         log: bool = True,
@@ -269,7 +270,7 @@ def _format_and_validate_names(
         format_sub = formatting.check_and_format_names(
             sub_names,
             "sub",
-            validation_templates,
+            name_templates,
             bypass_validation,
             allow_letters_in_sub_ses_values,
         )
@@ -278,7 +279,7 @@ def _format_and_validate_names(
             format_ses = formatting.check_and_format_names(
                 ses_names,
                 "ses",
-                validation_templates,
+                name_templates,
                 bypass_validation,
                 allow_letters_in_sub_ses_values,
             )
@@ -294,7 +295,7 @@ def _format_and_validate_names(
                 include_central=False,
                 display_mode="error",
                 log=log,
-                validation_templates=validation_templates,
+                name_templates=name_templates,
                 allow_letters_in_sub_ses_values=allow_letters_in_sub_ses_values,
             )
 
@@ -819,27 +820,47 @@ def setup_ssh_connection(self) -> None:
             "setup-ssh-connection-to-central-server", local_vars=locals()
         )
 
-        verified = ssh.verify_ssh_central_host_api(
+        verified = ssh.verify_ssh_central_host(
             self.cfg["central_host_id"],
             self.cfg.hostkeys_path,
             log=True,
         )
 
         if verified:
-            private_key_str = ssh.setup_ssh_key_api(self.cfg, log=True)
-
-            self._setup_rclone_central_ssh_config(private_key_str, log=True)
+            ssh.setup_ssh_key(self.cfg, log=True)
+            self._setup_rclone_central_ssh_config(log=True)
 
             rclone.check_successful_connection_and_raise_error_on_fail(
                 self.cfg
             )
 
-            utils.log_and_message(
-                "SSH key pair setup successfully. SSH key saved to the RClone config file."
-            )
-
         ds_logger.close_log_filehandler()
 
+    @requires_ssh_configs
+    @check_is_not_local_project
+    def write_public_key(self, filepath: str) -> None:
+        """Save the public SSH key to a specified filepath.
+
+        By default, only the SSH private key is stored in the
+        datashuttle configs folder. Use this function to save
+        the public key.
+
+        Parameters
+        ----------
+        filepath
+            Full filepath (including filename) to write the
+            public key to.
+
+        """
+        key: paramiko.RSAKey
+        key = paramiko.RSAKey.from_private_key_file(
+            self.cfg.ssh_key_path.as_posix()
+        )
+
+        with open(filepath, "w") as public:
+            public.write(key.get_base64())
+        public.close()
+
     # -------------------------------------------------------------------------
     # Google Drive
     # -------------------------------------------------------------------------
@@ -1056,17 +1077,7 @@ def make_config_file(
         ds_logger.close_log_filehandler()
 
     def update_config_file(self, **kwargs) -> None:
-        """Update the configuration file.
-
-        Parameters
-        ----------
-        **kwargs
-            A dictionary of key-value pairs containing the config
-            settings to update. For example,
-            ``{"connection_method": "local_filesystem", "central_path": "/my/local/path"}``
-            will update the ``connection_method`` and ``central_path`` settings.
-
-        """
+        """Update the configuration file."""
         if not self.cfg:
             utils.log_and_raise_error(
                 "Must have a config loaded before updating configs.",
@@ -1166,9 +1177,9 @@ def get_next_sub(
         The next subject ID.
 
         """
-        validation_template = self.get_validation_templates()
-        validation_template_regexp = (
-            validation_template["sub"] if validation_template["on"] else None
+        name_template = self.get_name_templates()
+        name_template_regexp = (
+            name_template["sub"] if name_template["on"] else None
         )
 
         if self.is_local_project():
@@ -1181,7 +1192,7 @@ def get_next_sub(
             include_central=include_central,
             return_with_prefix=return_with_prefix,
             search_str="sub-*",
-            validation_template_regexp=validation_template_regexp,
+            name_template_regexp=name_template_regexp,
         )
 
     @check_configs_set
@@ -1215,9 +1226,9 @@ def get_next_ses(
         The next session ID.
 
         """
-        validation_template = self.get_validation_templates()
-        validation_template_regexp = (
-            validation_template["ses"] if validation_template["on"] else None
+        name_template = self.get_name_templates()
+        name_template_regexp = (
+            name_template["ses"] if name_template["on"] else None
         )
 
         if self.is_local_project():
@@ -1230,7 +1241,7 @@ def get_next_ses(
             include_central=include_central,
             return_with_prefix=return_with_prefix,
             search_str="ses-*",
-            validation_template_regexp=validation_template_regexp,
+            name_template_regexp=name_template_regexp,
         )
 
     @check_configs_set
@@ -1245,38 +1256,36 @@ def is_local_project(self) -> bool:
     # Name Templates
     # -------------------------------------------------------------------------
 
-    def get_validation_templates(self) -> Dict:
+    def get_name_templates(self) -> Dict:
         """Return the regexp templates used for validation.
 
         If the "on" key is set to `False`, template validation is not performed.
 
         Returns
         -------
-        validation_templates
-            e.g. {"validation_templates": {"on": False, "sub": None, "ses": None}}
+        name_templates
+            e.g. {"name_templates": {"on": False, "sub": None, "ses": None}}
 
         """
         settings = self._load_persistent_settings()
-        return settings["validation_templates"]
+        return settings["name_templates"]
 
-    def set_validation_templates(self, new_validation_templates: Dict) -> None:
+    def set_name_templates(self, new_name_templates: Dict) -> None:
         """Update the persistent settings with new name templates.
 
-        Name templates are regexp for that, when ``validation_templates["on"]`` is
+        Name templates are regexp for that, when ``name_templates["on"]`` is
         set to ``True``, ``"sub"`` and ``"ses"`` names are validated against
         the regexp contained in the dict.
 
         Parameters
         ----------
-        new_validation_templates
-            e.g. ``{"validation_templates": {"on": False, "sub": None, "ses": None}}``
+        new_name_templates
+            e.g. ``{"name_templates": {"on": False, "sub": None, "ses": None}}``
             where ``"sub"`` or ``"ses"`` can be a regexp that subject and session
             names respectively are validated against.
 
         """
-        self._update_persistent_setting(
-            "validation_templates", new_validation_templates
-        )
+        self._update_persistent_setting("name_templates", new_name_templates)
 
     # -------------------------------------------------------------------------
     # Showers
@@ -1357,7 +1366,7 @@ def validate_project(
             local_vars=locals(),
         )
 
-        validation_templates = self.get_validation_templates()
+        name_templates = self.get_name_templates()
 
         if self.is_local_project():
             include_central = False
@@ -1371,7 +1380,7 @@ def validate_project(
             top_level_folder_to_validate,
             include_central=include_central,
             display_mode=display_mode,
-            validation_templates=validation_templates,
+            name_templates=name_templates,
             strict_mode=strict_mode,
             allow_letters_in_sub_ses_values=allow_letters_in_sub_ses_values,
         )
@@ -1569,13 +1578,11 @@ def _make_project_metadata_if_does_not_exist(self) -> None:
         """
         folders.create_folders(self.cfg.project_metadata_path, log=False)
 
-    def _setup_rclone_central_ssh_config(
-        self, private_key_str: str, log: bool
-    ) -> None:
+    def _setup_rclone_central_ssh_config(self, log: bool) -> None:
         rclone.setup_rclone_config_for_ssh(
             self.cfg,
             self.cfg.get_rclone_config_name("ssh"),
-            private_key_str,
+            self.cfg.ssh_key_path,
             log=log,
         )
 
@@ -1671,15 +1678,8 @@ def _update_settings_with_new_canonical_keys(self, settings: Dict) -> None:
         Added keys:
             v0.4.0: tui "overwrite_existing_files" and "dry_run"
         """
-        if "validation_templates" not in settings:
-            if "name_templates" in settings:
-                settings["validation_templates"] = settings.pop(
-                    "name_templates"
-                )
-            else:
-                settings.update(
-                    canonical_configs.get_validation_templates_defaults()
-                )
+        if "name_templates" not in settings:
+            settings.update(canonical_configs.get_name_templates_defaults())
 
         canonical_tui_configs = canonical_configs.get_tui_config_defaults()
 

datashuttle/datashuttle_functions.py

@@ -27,7 +27,7 @@ def validate_project_from_path(
     top_level_folder: Optional[TopLevelFolder] = "rawdata",
     display_mode: DisplayMode = "warn",
     strict_mode: bool = False,
-    validation_templates: Optional[Dict] = None,
+    name_templates: Optional[Dict] = None,
     allow_letters_in_sub_ses_values: bool = False,
 ) -> List[str]:
     """Perform validation on a NeuroBlueprint-formatted project.
@@ -54,9 +54,9 @@ def validate_project_from_path(
         any folder not prefixed with sub-, ses- or a valid datatype will
         raise a validation issue.
 
-    validation_templates
+    name_templates
         A dictionary of templates for subject and session name
-        to validate against. See ``DataShuttle.set_validation_templates()``
+        to validate against. See ``DataShuttle.set_name_templates()``
         for details.
 
     allow_letters_in_sub_ses_values
@@ -101,7 +101,7 @@ def validate_project_from_path(
         top_level_folder_list=top_level_folders_to_validate,
         include_central=False,
         display_mode=display_mode,
-        validation_templates=validation_templates,
+        name_templates=name_templates,
         strict_mode=strict_mode,
         allow_letters_in_sub_ses_values=allow_letters_in_sub_ses_values,
     )