junifer 0.0.4.dev8__tar.gz → 0.0.4.dev15__tar.gz

{junifer-0.0.4.dev8 → junifer-0.0.4.dev15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev8
+Version: 0.0.4.dev15
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.4.dev15/docs/changes/newsfragments/233.bugfix

@@ -0,0 +1 @@
+Adapt ``junifer queue`` to properly use HTCondor >=10.4.0 ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_

junifer-0.0.4.dev15/docs/changes/newsfragments/248.change

@@ -0,0 +1 @@
+Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon Mandal`_

junifer-0.0.4.dev15/junifer/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.0.4.dev15'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev15')

{junifer-0.0.4.dev8 → junifer-0.0.4.dev15}/junifer/api/functions.py

@@ -532,10 +532,12 @@ def _queue_condor(
     # Submit job(s)
     if submit is True:
         logger.info("Submitting HTCondor job")
-        subprocess.run(["condor_submit_dag", dag_fname])
+        subprocess.run(
+            ["condor_submit_dag", "-include_env", "HOME", dag_fname]
+        )
         logger.info("HTCondor job submitted")
     else:
-        cmd = f"condor_submit_dag {dag_fname.absolute()!s}"
+        cmd = f"condor_submit_dag -include_env 'HOME' {dag_fname.absolute()!s}"
         logger.info(
             f"HTCondor job files created, to submit the job, run `{cmd}`"
         )

{junifer-0.0.4.dev8 → junifer-0.0.4.dev15}/junifer/onthefly/read_transform.py

@@ -17,8 +17,9 @@ if TYPE_CHECKING:
 
 def read_transform(
     storage: Type["BaseFeatureStorage"],
-    feature_name: str,
     transform: str,
+    feature_name: Optional[str] = None,
+    feature_md5: Optional[str] = None,
     transform_args: Optional[Tuple] = None,
     transform_kw_args: Optional[Dict] = None,
 ) -> pd.DataFrame:
@@ -28,11 +29,13 @@ def read_transform(
     ----------
     storage : storage-like
         The storage class, for example, SQLiteFeatureStorage.
-    feature_name : str
-        Name of the feature to read.
     transform : str
         The kind of transform formatted as ``<package>_<function>``,
         for example, ``bctpy_degrees_und``.
+    feature_name : str, optional
+        Name of the feature to read (default None).
+    feature_md5 : str, optional
+        MD5 hash of the feature to read (default None).
     transform_args : tuple, optional
         The positional arguments for the callable of ``transform``
         (default None).
@@ -62,7 +65,9 @@ def read_transform(
     transform_kw_args = transform_kw_args or {}
 
     # Read storage
-    stored_data = storage.read(feature_name=feature_name)  # type: ignore
+    stored_data = storage.read(
+        feature_name=feature_name, feature_md5=feature_md5
+    )  # type: ignore
     # Retrieve package and function
     package, func_str = transform.split("_", 1)
     # Condition for package
@@ -105,7 +110,8 @@ def read_transform(
         # Apply function and store subject-wise
         output_list = []
         logger.debug(
-            f"Computing '{package}.{func_str}' for feature {feature_name} ..."
+            f"Computing '{package}.{func_str}' for feature "
+            f"{feature_name or feature_md5} ..."
         )
         for subject in range(stored_data["data"].shape[2]):
             output = func(
@@ -119,7 +125,8 @@ def read_transform(
         idx_df = pd.DataFrame(data=stored_data["element"])
         # Create multiindex from dataframe
         logger.debug(
-            f"Generating pandas.MultiIndex for feature {feature_name} ..."
+            "Generating pandas.MultiIndex for feature "
+            f"{feature_name or feature_md5} ..."
         )
         data_idx = pd.MultiIndex.from_frame(df=idx_df)
 

{junifer-0.0.4.dev8 → junifer-0.0.4.dev15}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev8
+Version: 0.0.4.dev15
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.4.dev8 → junifer-0.0.4.dev15}/junifer.egg-info/SOURCES.txt

@@ -56,7 +56,9 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
+docs/changes/newsfragments/233.bugfix
 docs/changes/newsfragments/247.doc
+docs/changes/newsfragments/248.change
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst

junifer-0.0.4.dev8/junifer/_version.py

@@ -1,4 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-__version__ = version = '0.0.4.dev8'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev8')