junifer 0.0.5.dev161__tar.gz → 0.0.5.dev164__tar.gz

{junifer-0.0.5.dev161 → junifer-0.0.5.dev164}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev161
+Version: 0.0.5.dev164
 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-0.0.5.dev164/docs/changes/newsfragments/327.doc

@@ -0,0 +1 @@
+Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_

{junifer-0.0.5.dev161 → junifer-0.0.5.dev164}/docs/using/queueing.rst

@@ -10,10 +10,10 @@ computational clusters. This is done by adding the ``queue`` section in the
 :ref:`codeless` file and executing the  ``junifer queue`` command.
 
 While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing
-using `GNU Parallel`_, only HTCondor is currently supported. This will be
-implemented in future releases of ``junifer``. If you are in immediate need of
-any of these schedulers, please create an issue on the `junifer github`_
-repository.
+using `GNU Parallel`_, only ``HTCondor`` and ``GNU Parallel`` are currently
+supported. This will be implemented in future releases of ``junifer``. If you are
+in immediate need of any of these schedulers, please create an issue on the
+`junifer github`_ repository.
 
 The ``queue`` section of the :ref:`codeless` must start by defining the
 following general parameters:
@@ -22,8 +22,8 @@ following general parameters:
   folder where the job files will be created, as well as any relevant file.
   Depending on the scheduler, it will also be listed in the queueing system
   with this name.
-* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` is
-  supported.
+* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` and
+  ``GNUParallelLocal`` are supported.
 
 Example in YAML:
 
@@ -48,7 +48,9 @@ jobs are finished.
 
 The following parameters are available for HTCondor:
 
-* ``env``: Definition of the Python environment. It must provide two variables:
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
 
   * ``kind``: This is the kind of virtual environment to use:
 
@@ -61,6 +63,9 @@ The following parameters are available for HTCondor:
     the absolute or relative path to the virtualenv when ``venv`` is used.
     If relative path is used then it should be relative to the YAML.
 
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
 * ``mem``: Memory to be used by the job. It must be provided as a string with
   the units (e.g., ``"2GB"``).
 * ``cpus``: Number of CPUs to be used by the job. It must be provided as an
@@ -93,10 +98,78 @@ Example in YAML:
     env:
       kind: conda
       name: junifer
+      shell: zsh
+    mem: 8G
+    disk: 2G
+    collect: "yes"  # wrap it in string to avoid boolean
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestHTCondorQueue
+    kind: HTCondor
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
     mem: 8G
     disk: 2G
     collect: "yes"  # wrap it in string to avoid boolean
 
+.. _queueing_local:
+
+GNUParallelLocal
+----------------
+
+When using GNU Parallel, ``junifer`` will run only in local mode and leverage
+maximum computational power of whatever hardware it is run on.
+
+The following parameters are available for GNUParallelLocal:
+
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
+
+  * ``kind``: This is the kind of virtual environment to use:
+
+    * ``conda``
+    * ``venv``
+    * ``local`` (no virtual environment)
+
+  * ``name``: This is the name of the environment to use in case a virtual
+    environment is used. It should be the name when ``conda`` is used and
+    the absolute or relative path to the virtualenv when ``venv`` is used.
+    If relative path is used then it should be relative to the YAML.
+
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
+Example in YAML:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: conda
+      name: junifer
+      shell: zsh
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
+
 Once the :ref:`codeless` file is ready, including the ``queue`` section, you can
 queue the jobs by executing the ``junifer queue`` command.
 

{junifer-0.0.5.dev161 → junifer-0.0.5.dev164}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev161'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev161')
+__version__ = version = '0.0.5.dev164'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev164')

{junifer-0.0.5.dev161 → junifer-0.0.5.dev164}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev161
+Version: 0.0.5.dev164
 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-0.0.5.dev161 → junifer-0.0.5.dev164}/junifer.egg-info/SOURCES.txt

@@ -63,6 +63,7 @@ docs/changes/newsfragments/161.feature
 docs/changes/newsfragments/273.feature
 docs/changes/newsfragments/323.feature
 docs/changes/newsfragments/324.bugfix
+docs/changes/newsfragments/327.doc
 docs/changes/newsfragments/330.doc
 docs/changes/newsfragments/331.bugfix
 docs/changes/newsfragments/332.bugfix