Update docs to PEPENV

doc/source/changelog.rst

@@ -19,6 +19,8 @@ Changelog
 
   - Changed
 
+    - Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models
+
     - Changed name of ``run`` column to ``toggle``, since ``run`` can also refer to a sequencing run.
 
     - Relaxes many constraints (like resources sections, pipelines_dir columns), making project

doc/source/cluster-computing.rst

@@ -5,7 +5,7 @@ Cluster computing
 
 By default, looper will build a shell script for each sample and then run each sample serially on the local computer. But where looper really excels is in large projects that require submitting these jobs to a cluster resource manager (like SLURM, SGE, LFS, etc.). Looper handles the interface to the resource manager so that projects and pipelines can be moved to different environments with ease. 
 
-To configure looper to use cluster computing, all you have to do is tell looper a few things about your cluster setup: you create a configuration file (`compute_config.yaml`) and point an environment variable (``LOOPERENV``) to this file, and that's it! Complete, step-by-step instructions and examples are available in the looperenv repository at https://github.com/epigen/looperenv.
+To configure looper to use cluster computing, all you have to do is tell looper a few things about your cluster setup: you create a configuration file (`compute_config.yaml`) and point an environment variable (``PEPENV``) to this file, and that's it! Complete, step-by-step instructions and examples are available in the pepenv repository at https://github.com/pepkit/pepenv.
 
 Compute config overview 
 ****************************************
@@ -31,12 +31,12 @@ The sub-sections below ``compute`` each define a "compute package" that can be a
 
 There are two or three sub-parameters for a compute package:
 
-   - **submission_template** is a (relative or absolute) path to the template submission script. Templates are described in more detail in the `looperenv readme <https://github.com/epigen/looperenv>`_. 
+   - **submission_template** is a (relative or absolute) path to the template submission script. Templates are described in more detail in the `pepenv readme <https://github.com/pepkit/pepenv>`_. 
    - **submission_command** is the command-line command that `looper` will prepend to the path of the produced submission script to actually run it (`sbatch` for SLURM, `qsub` for SGE, `sh` for localhost, etc).
    - **partition** is necessary only if you need to specify a queue name
 
 
 Submission templates
 ****************************************
-A template uses variables (encoded like `{VARIABLE}`), which will be populated independently for each sample as defined in `pipeline_interface.yaml`. The one variable ``{CODE}`` is a reserved variable that refers to the actual python command that will run the pipeline. Otherwise, you can use any variables you define in your `pipeline_interface.yaml`. In `Templates <https://github.com/epigen/looperenv/tree/master/templates>`__ are examples for submission templates for `SLURM <https://github.com/epigen/looperenv/blob/master/templates/slurm_template.sub>`__, `SGE <https://github.com/epigen/looperenv/blob/master/templates/sge_template.sub>`__, and `local runs <https://github.com/epigen/looperenv/blob/master/templates/localhost_template.sub>`__. You can also create your own templates, giving looper ultimate flexibility to work with any compute infrastructure in any environment.
+A template uses variables (encoded like `{VARIABLE}`), which will be populated independently for each sample as defined in `pipeline_interface.yaml`. The one variable ``{CODE}`` is a reserved variable that refers to the actual python command that will run the pipeline. Otherwise, you can use any variables you define in your `pipeline_interface.yaml`. In `Templates <https://github.com/pepkit/pepenv/tree/master/templates>`__ are examples for submission templates for `SLURM <https://github.com/pepkit/pepenv/blob/master/templates/slurm_template.sub>`__, `SGE <https://github.com/pepkit/pepenv/blob/master/templates/sge_template.sub>`__, and `local runs <https://github.com/pepkit/pepenv/blob/master/templates/localhost_template.sub>`__. You can also create your own templates, giving looper ultimate flexibility to work with any compute infrastructure in any environment.
 

doc/source/project-config.rst

@@ -129,7 +129,7 @@ The above specification will now pass '--flavor=simple' and '--flag' whenever rr
 
 Project config section: compute
 """""""""""""""""""""""""""""""""""""""""""""""
-You can specify project-specific compute settings in a ``compute`` section. However, you're better off specifying this globally using a ``looperenv`` environment configuration. Instructions are at the `looperenv repository <https://github.com/epigen/looperenv>`_. If you do need project-specific control over compute settings (like submitting a certain project to a certain resource account), you can do this by specifying variables in a project config ``compute`` section, which will override global looperenv values for that project only.
+You can specify project-specific compute settings in a ``compute`` section. However, you're better off specifying this globally using a ``pepenv`` environment configuration. Instructions are at the `pepenv repository <https://github.com/pepkit/pepenv>`_. If you do need project-specific control over compute settings (like submitting a certain project to a certain resource account), you can do this by specifying variables in a project config ``compute`` section, which will override global pepenv values for that project only.
 
 
 .. code-block:: yaml