update docs

docs/tutorial_developers.rst

@@ -4,19 +4,19 @@ Tutorial for WC modeling software developers
 Creating a new package
 ----------------------
 
-Run this command to create a new package (create local and remote repositories with the proper directory structure and files for our build system, add repository to CircleCI, add package to downstream dependencies of dependencies, etc.). The command will prompt you for all of the information needed to create a repository and instruct you how to create a new package, including linking it to CircleCI, Coveralls, Code Climate, and Read the Docs. The command should be run from the package's desired parent directory, e.g. with a current working directory of ``~/Documents``.::
+Run ``create-package`` to create a new package (create local and remote repositories with the proper directory structure and files for our build system, add repository to CircleCI, add the package to downstream dependencies of dependent packages, etc.). The command will prompt you for all of the information needed to create a repository and instruct you how to create a new package, including linking it to `CircleCI<https://circleci.com/product/>_`, `Coveralls<https://coveralls.io>_`, `Code Climate<https://codeclimate.com/quality/>_`, and `Read the Docs<https://readthedocs.org>_`. The command should be run from the package's desired parent directory, e.g. with a current working directory of ``~/git_repositories``.::
 
-    cd ~/Documents
+    cd ~/git_repositories
     karr_lab_build_utils create-package
 
-``karr_lab_build_utils`` also provides two lower-level commands for creating, cloning, and initializing Git repositories. These commands are an alternative to the ``create-package`` command which creates, clones, and initializes Git repositories and much more.
+``karr_lab_build_utils`` also provides two lower-level commands for creating, cloning, and initializing Git repositories. These commands are an alternative to the ``create-package`` command which does much more.
 
 * ``create-repository``: create a new GitHub repository and clone it locally
 * ``setup-repository``: set up the file structure of a local Git repository
 
 .. code::
 
-    cd ~/Documents
+    cd ~/git_repositories
     karr_lab_build_utils create-repository
     karr_lab_build_utils setup-repository
 
@@ -55,6 +55,7 @@ Please see the `Software engineering <https://docs.karrlab.org/intro_to_wc_model
 Managing dependencies of packages
 ---------------------------------
 
+
 Installing the dependencies for a package
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -72,9 +73,9 @@ Run the following command to install all of the requirements for the current pac
 Finding missing requirements for a package
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Run this command to find potentially missing requirements for a package::
+Run this command to find potentially missing requirements for the package ``package_name``::
 
-    karr_lab_build_utils find-missing-requirements
+    karr_lab_build_utils find-missing-requirements package_name
 
 Finding unused requirements for a package
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -89,19 +90,19 @@ Compiling the downstream dependencies of a package
 #. Clone all of our packages
 #. Run this command to compile the downstream dependencies of your package::
 
-    karr_lab_build_utils compile-downstream-dependencies --packages-parent-dir ~/Documents
+    karr_lab_build_utils compile-downstream-dependencies --packages-parent-dir ~/git_repositories
 
 #. Optionally, add the ``--downstream-dependencies-filename`` option to save the dependencies to a YAML file::
 
-    karr_lab_build_utils compile-downstream-dependencies --packages-parent-dir ~/Documents --downstream-dependencies-filename .circleci/downstream_dependencies.yml
+    karr_lab_build_utils compile-downstream-dependencies --packages-parent-dir ~/git_repositories --downstream-dependencies-filename .circleci/downstream_dependencies.yml
 
 
 Configuring packages
 ---------------------------
 
-The ``karr_lab_build_config`` repository should contain all of the whole-cell modeling and third party configuration files needed to run your tests. This should include all usernames, passwords, and tokens needed to run your tests.
+The ``karr_lab_build_config`` repository should contain all of the whole-cell modeling and third party access credentials and configuration files needed to run your tests. This should include all usernames, passwords, and tokens needed to run your tests.
 
-Configuration files for whole-cell modeling software should be saved to the top-level directory of the ``karr_lab_build_config`` repository with the file pattern ``<package_name>.cfg``. 
+Configuration files for whole-cell modeling packages should be saved to the top-level directory of the ``karr_lab_build_config`` repository with the file pattern ``<package_name>.cfg``. 
 
 All configuration files for third-party software should be saved to the ``third_party`` subdirectory of the ``karr_lab_build_config`` repository. In addition, ``third_party/paths.yml`` should contain a YAML-formatted dictionary whose keys are the names of the files in the ``third_party`` subdirectory and whose values are the locations that these files should be copied to.