Fix typos and grammar in documentation

CODE_OF_CONDUCT.rst

@@ -3,7 +3,7 @@ Pulsar Project Code of Conduct
 ------------------------------
 
 This code of conduct outlines our expectations for participants within the
-Pulsar community, as well as steps to reporting unacceptable behavior. We are
+Pulsar community, as well as steps for reporting unacceptable behavior. We are
 committed to providing a welcoming and inspiring community for all and expect
 our code of conduct to be honored. Anyone who violates this code of conduct may
 be banned from the community.
@@ -19,7 +19,7 @@ Our open source community strives to:
   orientation, gender identity and expression, age, size, family status,
   political belief, religion, and mental and physical ability.
 
-* **Be considerate**: Your work will be used by other people, and you in turn
+* **Be considerate**: Your work will be used by other people, and you, in turn,
   will depend on the work of others. Any decision you take will affect users
   and colleagues, and you should take those consequences into account when
   making decisions. Remember that we're a world-wide community, so you might
@@ -34,13 +34,13 @@ Our open source community strives to:
 * **Be careful in the words that we choose**: We are a community of
   professionals, and we conduct ourselves professionally. Be kind to others. Do
   not insult or put down other participants. Harassment and other exclusionary
-  behavior aren't acceptable. This includes, but is not limited to: Violent
-  threats or language directed against another person, Discriminatory jokes and
-  language, Posting sexually explicit or violent material, Posting (or
+  behavior aren't acceptable. This includes, but is not limited to: violent
+  threats or language directed against another person, discriminatory jokes and
+  language, posting sexually explicit or violent material, posting (or
   threatening to post) other people’s personally identifying information
-  (“doxing”), Personal insults, especially those using racist or sexist terms,
-  Unwelcome sexual attention, Advocating for, or encouraging, any of the above
-  behavior, Repeated harassment of others. In general, if someone asks you to
+  (“doxing”), personal insults, especially those using racist or sexist terms,
+  unwelcome sexual attention, advocating for, or encouraging, any of the above
+  behavior, repeated harassment of others. In general, if someone asks you to
   stop, then stop.
 
 * **Try to understand why we disagree**: Disagreements, both social and
@@ -57,7 +57,7 @@ Diversity Statement
 -------------------
 
 We encourage everyone to participate and are committed to building a community
-for all. Although we will fail at times, we seek to treat everyone both as
+for all. Although we will fail at times, we seek to treat everyone as
 fairly and equally as possible. Whenever a participant has made a mistake, we
 expect them to take responsibility for it. If someone has been harmed or
 offended, it is our responsibility to listen carefully and respectfully, and do
@@ -80,7 +80,7 @@ the most comfortable:
 - Dave Clements (clementsgalaxy@gmail.com). Dave is the Galaxy Project community
   outreach manager and has experience handling Code of Conduct related issues.
 - Dr. Mike Schatz (mschatz@cs.jhu.edu). Mike is Dave Clements' direct manager
-  and issues related to Dave in some way should be reported to Mike.
+  and issues related to Dave, in some ways, should be reported to Mike.
 - Helena Rasche (helena.rasche@gmail.com). Helena is a well-known, trusted
   community member, is LGBT+, and has completely separate funding and
   institutional affiliation from Dave and Mike.

CONTRIBUTING.rst

@@ -2,9 +2,8 @@
 Contributing
 ============
 
-Please note that this project is released with a `Contributor Code of Conduct
-<https://pulsar.readthedocs.org/en/latest/conduct.html>`. By participating in
-this project you agree to abide by its terms.
+Please note that this project is released with a `Contributor Code of Conduct <https://pulsar.readthedocs.org/en/latest/conduct.html>`_. By participating in
+this project, you agree to abide by its terms.
 
 Contributions are welcome, and they are greatly appreciated! Every
 little bit helps, and credit will always be given.
@@ -21,7 +20,7 @@ Report bugs at https://github.com/galaxyproject/pulsar/issues.
 
 If you are reporting a bug, please include:
 
-* Your operating system name and version, versions of other relevant software 
+* Your operating system name and version, along with versions of any other relevant software, 
   such as Galaxy or Docker.
 * Links to relevant tools.
 * Any details about your local setup that might be helpful in troubleshooting.
@@ -31,19 +30,19 @@ Fix Bugs
 ~~~~~~~~
 
 Look through the GitHub issues for bugs. Most things there are up for grabs
-but the tag "Help Wanted" may be particulary good places to start.
+but the tag "Help Wanted" may be a particularly good place to start.
 
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
 Look through the GitHub issues for features (tagged with "enhancement").
 Again, most things there are up for grabs but the tag "Help Wanted" may be
-particulary good places to start.
+a particularly good place to start.
 
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-Pulsar is cronically under documented, whether as part of the
+Pulsar is chronically under documented, whether as part of the
 official Pulsar docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
@@ -55,7 +54,7 @@ The best way to send feedback is to file an issue at https://github.com/galaxypr
 If you are proposing a feature:
 
 * Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
+* Keep the scope as narrow as possible to make it easier to implement.
 * This will hopefully become a community-driven project and contributions
   are welcome :)
 
@@ -89,15 +88,15 @@ Ready to contribute? Here's how to set up `pulsar` for local development.
 
     $ make lint
 
-and ensure the tests look good. The easiest way to test is with Docker if it is
+And ensure the tests look good. The easiest way to test is with Docker if it is
 available (given the need to test commands with DRMAA, condor, sudo, etc...).::
 
     $ docker run -v `pwd`:/pulsar -t jmchilton/pulsar_testing
 
 This will mount your copy of `pulsar` in a Docker container preconfigured with all
 optional dependencies needed to run a wide range of integration tests. If Docker
-is to much of an ordeal many of Pulsar's tests can be executed by simply running 
-``pytest`` from within an ``virtualenv`` configured as explained above.::
+is too much of an ordeal, many of Pulsar's tests can be executed by simply running 
+``pytest`` from within a ``virtualenv`` configured as explained above.::
 
     $ make tests
 

README.rst

@@ -16,7 +16,7 @@
 
 This project is a Python server application that allows a `Galaxy
 <http://galaxyproject.org>`_ server to run jobs on remote systems (including
-Windows) without requiring a shared mounted file systems. Unlike traditional
+Windows) without requiring a shared mounted file system. Unlike traditional
 Galaxy job runners - input files, scripts, and config files may be transferred
 to the remote system, the job is executed, and the results are transferred back
 to the Galaxy server - eliminating the need for a shared file system.
@@ -42,8 +42,8 @@ Quickstart
 
 Full details on different ways to install Pulsar can be found in the `install
 section <https://pulsar.readthedocs.org/en/latest/install.html>`__ of the
-documentaiton, but if your machine has the proper Python dependencies
-available it can be quickly download and a test job run with::
+documentation, but if your machine has the proper Python dependencies
+available, it can be quickly downloaded and a test job runs with::
 
     $ mkdir pulsar
     $ cd pulsar
@@ -67,7 +67,7 @@ Development and Testing
 -----------------------
 
 The recommended approach to setting up a development environment for Pulsar on
-Linux or macOS is rougly as follows::
+Linux or macOS is roughly as follows::
 
     $ git clone https://github.com/galaxyproject/pulsar
     $ cd pulsar
@@ -81,7 +81,7 @@ changes you make to the source code will be reflected when running the pulsar
 commands installed in the virtual environment.
 
 This project is distributed with unit and integration tests (many of which will
-not run under Windows), the following command will install the needed python
+not run under Windows). The following command will install the needed python
 components to run these tests. The following command will then run these tests::
 
     $ make tests
@@ -98,7 +98,7 @@ for many more details on developing and contributing to Pulsar.
 
 Please note that this project is released with a `Contributor Code of Conduct 
 <https://pulsar.readthedocs.org/en/latest/conduct.html>`__. By participating
-in this project you agree to abide by its terms.
+in this project, you agree to abide by its terms.
 
 -----------------------
 Support
@@ -107,7 +107,7 @@ Support
 This documentation is an incomplete work in progress. There are more ways to
 configure and use Pulsar than are documented, and a growing number of Pulsar
 experts who would be more than happy to answer your questions and help with any
-problems you may run in to while setting up a Pulsar deployment. Please do not
+problems you may run into while setting up a Pulsar deployment. Please do not
 hesitate to reach out on the `Galaxy Admins Gitter Channel`_
 
 .. _Galaxy Admins Gitter Channel: https://gitter.im/galaxyproject/admins

dev-requirements.txt

@@ -22,6 +22,7 @@ sphinxcontrib-apidoc
 # Used for code checking.
 pyflakes
 flake8
+tox
 
 mypy
 types-paramiko

docs/configure.rst

@@ -29,7 +29,7 @@ Security
 
 Out of the box, **Pulsar essentially allows anyone with network access to the
 Pulsar server to execute arbitrary code and read and write any files the web
-server can access.** Hence, in most settings steps should be taken to secure the
+server can access.** Hence, in most settings, steps should be taken to secure the
 Pulsar server.
 
 Private Token
@@ -52,19 +52,19 @@ use.
 
 .. tip::
 
-    SSL support is built in to `uWSGI`_, an alternate webserver that can be
+    SSL support is built in to `uWSGI`_, an alternate web server that can be
     installed (see :ref:`install`).
 
 ``pyOpenSSL`` is required to configure a Pulsar web server to server content via
 HTTPS/SSL. This dependency can be difficult to install and seems to be getting
 more difficult. Under Linux you will want to ensure the needed dependencies to
-compile pyOpenSSL are available - for instance in a fresh Ubuntu image you
+compile pyOpenSSL are available - for instance, in a fresh Ubuntu image, you
 will likely need::
 
     $ sudo apt-get install libffi-dev python3-dev libssl-dev
 
 Then pyOpenSSL can be installed with the following command (be sure to source
-your virtualenv if setup above)::
+your virtualenv if set up above)::
 
     $ pip install pyOpenSSL
 
@@ -119,8 +119,8 @@ You can configure Pulsar to authenticate user during request processing and chec
 if this user is allowed to run a job.
 
 Various authentication/authorization plugins can be configured in `app.yml` to
-do that and plugin parameters depend on auth type. For example, the following
-configuration uses `oidc` plugin for authentication and `userlist` for
+do that and plugin parameters depend on the auth type. For example, the following
+configuration uses the `oidc` plugin for authentication and `userlist` for
 authorization::
 
     user_auth:
@@ -136,7 +136,8 @@ authorization::
             - xxx
 
 
-see `plugins folder
+See the `plugins folder
+<https://github.com/galaxyproject/pulsar/blob/master/pulsar/user_auth/methods>`_
 <https://github.com/galaxyproject/pulsar/blob/master/pulsar/user_auth/methods>`_
 for available plugins and their parameters.
 
@@ -145,13 +146,13 @@ Customizing the Pulsar Environment (\*nix only)
 
 For many deployments, Pulsar's environment will need to be tweaked. For
 instance to define a ``DRMAA_LIBRARY_PATH`` environment variable for the
-``drmaa`` Python module or to define the location to a find a location of
+``drmaa`` Python module or to define the location to find a location of
 Galaxy (via ``GALAXY_HOME``) if certain Galaxy tools require it or if Galaxy
 metadata is being set by the Pulsar.
 
 The file ``local_env.sh`` (created automatically by ``pulsar-config``) will be
 source by ``pulsar`` before launching the application and by child process
-created by Pulsar that require this configuration.
+created by Pulsar that requires this configuration.
 
 Job Managers (Queues)
 ---------------------
@@ -222,7 +223,7 @@ In the event that the connection to the AMQP server is lost during message
 publish, the Pulsar server can retry the connection, governed by the
 ``amqp_publish*`` options documented in `app.yml.sample`_.
 
-Message Queue (pulsar-relay)
+Message queue (pulsar-relay)
 -----------------------------
 
 Pulsar can also communicate with Galaxy via an experimental **pulsar-relay** server,
@@ -528,4 +529,4 @@ and future plans and progress can be tracked on `this Trello card <https://trell
 .. _AMQP: http://en.wikipedia.org/wiki/AMQP
 .. _RabbitMQ: https://www.rabbitmq.com/
 .. _app.yml.sample: https://github.com/galaxyproject/pulsar/blob/master/app.yml.sample
-.. _Two Generals Problem: https://en.wikipedia.org/wiki/Two_Generals%27_Problem
+.. _Two Generals' Problem: https://en.wikipedia.org/wiki/Two_Generals%27_Problem