junifer 0.0.4.dev587__py3-none-any.whl → 0.0.4.dev594__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev587'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev587')
+__version__ = version = '0.0.4.dev594'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev594')

junifer/api/functions.py

@@ -418,7 +418,10 @@ def _queue_condor(
         env_name = env["name"]
         executable = "run_venv.sh"
         arguments = f"{env_name} junifer"
-        # TODO: Copy run_venv.sh to jobdir
+        exec_path = jobdir / executable
+        logger.info(f"Copying {executable} to {exec_path.absolute()!s}")
+        shutil.copy(Path(__file__).parent / "res" / executable, exec_path)
+        make_executable(exec_path)
     elif env["kind"] == "local":
         executable = "junifer"
         arguments = ""

junifer/api/parser.py

@@ -99,4 +99,17 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                 contents["storage"]["uri"] = str(
                     (filepath.parent / uri_path).resolve()
                 )
+
+    # Allow relative path if queue env kind is venv; same motivation as above
+    if "queue" in contents:
+        if "env" in contents["queue"]:
+            if "venv" == contents["queue"]["env"]["kind"]:
+                # Check if the env name is relative
+                venv_path = Path(contents["queue"]["env"]["name"])
+                if not venv_path.is_absolute():
+                    # Compute the absolute path
+                    contents["queue"]["env"]["name"] = str(
+                        (filepath.parent / venv_path).resolve()
+                    )
+
     return contents

junifer/api/res/run_conda.sh

@@ -1,17 +1,17 @@
 #!/bin/bash
 
 if [ $# -lt 2 ]; then
-    echo "This script is meant to run a command within a python environment"
+    echo "This script is meant to run a command within a conda environment."
     echo "It needs at least 2 parameters."
     echo "The first one must be the environment name."
-    echo "The rest will be the command"
+    echo "The rest will be the command."
     exit 255
 fi
 
 eval "$(conda shell.bash hook)"
 env_name=$1
 echo "Activating ${env_name}"
-conda activate "$1"
+conda activate "${env_name}"
 shift 1
 
 if [ -f "pre_run.sh" ]; then
@@ -19,5 +19,5 @@ if [ -f "pre_run.sh" ]; then
     . ./pre_run.sh
 fi
 
-echo "Running ${*} in virtual environment"
+echo "Running ${*} in conda environment"
 "$@"

junifer/api/res/run_venv.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+if [ $# -lt 2 ]; then
+    echo "This script is meant to run a command within a Python virtual environment."
+    echo "It needs at least 2 parameters."
+    echo "The first one must be the virtualenv path."
+    echo "The rest will be the command."
+    exit 255
+fi
+
+env_path=$1
+echo "Activating ${env_path}"
+source "${env_path}"/bin/activate
+shift 1
+
+if [ -f "pre_run.sh" ]; then
+    echo "Sourcing pre_run.sh"
+    . ./pre_run.sh
+fi
+
+echo "Running ${*} in Python virtual environment"
+"$@"

{junifer-0.0.4.dev587.dist-info → junifer-0.0.4.dev594.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev587
+Version: 0.0.4.dev594
 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.dev587.dist-info → junifer-0.0.4.dev594.dist-info}/RECORD

@@ -1,13 +1,14 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=jRCAqJ8XX2RVzioqqJ2HfV12Yo7uICU0v_bmiNBLdQs,428
+junifer/_version.py,sha256=Ji34482-PAWG6zwQO7I8NdFGpe6EM1-bfdOTbh3Sv4k,428
 junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=T6FTW3vDRlsdkSYerbQD7Q05uA9bV6f8oHvK1jxGUa8,12882
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
-junifer/api/functions.py,sha256=XSliwA2Q9NaplfYFcK9vy6G-B-EZz894ec9LsV2RA-s,23058
-junifer/api/parser.py,sha256=a0IBvH3KN1PJaEpF3cnSv8g7VCVpDY1VsCvc8b8FFmE,3849
+junifer/api/functions.py,sha256=ZNB9g7TRy6-r9U087sncKKD8ZGdQAgyplH4RHcZFRdU,23238
+junifer/api/parser.py,sha256=a3SSC2xO-PF1pqXZXFq8Sh9aVd-dmHolJbCkGyOUTAM,4416
 junifer/api/utils.py,sha256=dyjTdPMwX9qeCrn8SQT2Pjshfnu-y1FEyujV7lCzvm0,3333
-junifer/api/res/run_conda.sh,sha256=GerhBGReDw-_fp6RPnaorMHT9IHrp3LRgHJY4mgK4_Y,501
+junifer/api/res/run_conda.sh,sha256=eskIn-fotITOlh--IUQKXh-SBOZkDkK8QvDcdQsyJ0M,509
+junifer/api/res/run_venv.sh,sha256=OF-LOdOdpjCU0JX6Dz1boG4ErPutTiVVD_N7j520Fvk,499
 junifer/api/res/afni/3dAFNItoNIFTI,sha256=Fsy5S5rwIBb1MepLfl_5FQhE7gv6NDwNyAR_k036NmM,51
 junifer/api/res/afni/3dRSFC,sha256=MkPtS_nKEoJOHDAT3ZP9IA-SvMdhyzZDiyxObV_XI3g,44
 junifer/api/res/afni/3dReHo,sha256=Jb5B97iPPPQ14zAz7tK5BVG4jPZyOe9c6kgM6ixKaY8,44
@@ -234,10 +235,10 @@ junifer/utils/logging.py,sha256=T0HgiCI6cS2tp9nbI4cM3nVzMMjiVzgoxuyo5Y1rCyY,9124
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev587.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev587.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev587.dist-info/METADATA,sha256=oexdrhEQvCUgBCtdR2W2l0k5IDmyNQzsxMw9P5IfolY,8128
-junifer-0.0.4.dev587.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev587.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev587.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev587.dist-info/RECORD,,
+junifer-0.0.4.dev594.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev594.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev594.dist-info/METADATA,sha256=ARdjzo_GyiF8LMNkJZ3lnDrF2czE2b44g4ChzZhqjGk,8128
+junifer-0.0.4.dev594.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev594.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev594.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev594.dist-info/RECORD,,