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Merge pull request #1837 from dib-lab/fix/install-docs
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[MRG] Fix install docs
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@ctb
ctb committed Feb 11, 2018
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Expand Up @@ -55,48 +55,37 @@ particular, check out the
`git-scm book <http://git-scm.com/book/en/Git-Branching>`__. We've also provided
a quick guide to the khmer code base here: :doc:`codebase-guide`.

One-time Preparation
One-time preparation
--------------------

#. Install the dependencies.
#. Install prerequisites and set up a virtual environment following the :ref:`installation instructions in the user documentation <user_install_prereqs>`.

i. Mac users
.. note::

a. Install Xcode with::
DO NOT proceed to the final step and install khmer with pip!

xcode-select --install
#. Install additional prerequisites using your system's package manager.

#. Install `Homebrew <http://brew.sh/>`__ with::
a. Mac OS X

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install astyle gcovr cppcheck enchant

#. Install the python development environment and some additional development packages::
#. Debian / Ubuntu

brew install python astyle gcovr cppcheck enchant
sudo pip install --upgrade pip virtualenv
sudo apt-get install -y git astyle gcovr cppcheck enchant

ii. Linux users
#. Red Hat / Fedora / CentOS

Install the python development environment and some additional
development packages. On recent versions of Debian or Ubuntu this can
be done with::

sudo apt-get install python2.7-dev python-virtualenv python-pip \
gcc g++ git astyle gcovr cppcheck enchant

For Red Hat, Fedora, and CentOS::

sudo yum install -y python-devel python-pip git gcc gcc-c++ make enchant
sudo pip install virtualenv
sudo yum install -y git astyle gcovr cppcheck enchant

#. Create a `GitHub <http://github.com>`__ account.

We use GitHub to manage khmer contributions.

#. Fork `github.com/dib-lab/khmer <https://github.com/dib-lab/khmer>`__.

Visit that page, and then click on the 'fork' button (upper right). This
makes a copy of the khmer source code in your own GitHub account.
Visit that page, and then click on the 'fork' button (upper right).
This makes a copy of the khmer source code in your own GitHub account.

#. Clone your copy of khmer to your local development environment.

Expand All @@ -114,19 +103,14 @@ One-time Preparation
This makes it easy for you to pull down the latest changes in the
main repository.

#. Optional: create a virtual Python environment for khmer development
#. Install Python developement dependencies

See the **Virtual Environments** heading in :doc:`guidelines-continued-dev`
for more details on creating and using a virtual environment for development.
This is not strictly required but highly recommended, especially if you plan
to make continued contributions.
From within the khmer directory, invoke::

#. Install Python dependencies
make install-dep

From within the khmer directory, invoke the ``make install-dep`` command. If
you are not using a virtual environment, you may need to invoke ``sudo make
install-dep`` instead. This will install several packages used in khmer
testing and development.
If you have chosen not using a virtual environment, you may need to invoke ``sudo make install-dep`` instead.
This will install several packages used in khmer testing and development.


Building khmer and running the tests
Expand All @@ -136,17 +120,16 @@ Building khmer and running the tests

make

This compiles the C++ source code into something that Python can run. If the
command fails, we apologize—please `go create a new issue
<https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__,
paste in the failure message, and we'll try to help you work through it!
This compiles the C++ source code into something that Python can run.
If the command fails, we apologize!
Please `go create a new issue <https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__, paste in the failure message, and we'll try to help you work through it!

#. Run the tests::

make test

This will run all of the Python tests in the ``tests/`` directory. You should
see lots of output, with something like::
This will run all of the Python tests in the ``tests/`` directory.
You should see lots of output, with something like::

====== 1289 passed, 1 skipped, 25 deselected, 1 xpassed in 50.98 seconds =======

Expand All @@ -160,59 +143,48 @@ Claiming an issue and starting to develop

#. Find an open issue and claim it.

Go to `the list of open khmer issues
<https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__
and find one you like; we suggest starting with `the low-hanging fruit issues <https://github.com/dib-lab/khmer/issues?direction=desc&labels=low-hanging-fruit&page=1&sort=created&state=open>`__).
Go to `the list of open khmer issues <https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__ and find one you like; we suggest starting with `the low-hanging fruit issues <https://github.com/dib-lab/khmer/issues?direction=desc&labels=low-hanging-fruit&page=1&sort=created&state=open>`__).

Once you've found an issue you like, make sure that no one has been
assigned to it (see "assignee", bottom right near "notifications").
Then, add a comment "I am working on this issue." You've staked
your claim!
Once you've found an issue you like, make sure that no one has been assigned to it (see "assignee", bottom right near "notifications").
Then, add a comment "I am working on this issue."
You've staked your claim!

(We're trying to avoid having multiple people working on the same issue.)

#. In your local copy of the source code, update your master branch
from the main khmer master branch::
#. In your local copy of the source code, update your master branch from the main khmer master branch::

git checkout master
git pull dib master

(This pulls in all of the latest changes from whatever we've been
doing on dib-lab.)
(This pulls in all of the latest changes from whatever we've been doing on ``dib-lab``.)

If git complains about a "merge conflict" when you execute ``git pull``,
refer to the **Resolving merge conflicts** section of
:doc:`guidelines-continued-dev`.
If git complains about a "merge conflict" when you execute ``git pull``, refer to the **Resolving merge conflicts** section of :doc:`guidelines-continued-dev`.

#. Create a new branch and link it to your fork on GitHub::

git checkout -b fix/brief_issue_description
git push -u origin fix/brief_issue_description

where you replace "fix/brief_issue_description" with 2-3 words, separated
by underscores, describing the issue.
where you replace "fix/brief_issue_description" with 2-3 words, separated by underscores, describing the issue.

(This is the set of changes you're going to ask to be merged into khmer.)

#. Make some changes and commit them.

Though this will largely be issue-dependent the basics of committing are
simple. After you've made a cohesive set of changes, run the command `git
status`. This will display a list of all the files git has noticed you
changed. A file in the 'untracked' section are files that haven't existed
previously in the repository but git has noticed.
Though this will largely be issue-dependent the basics of committing are simple.
After you've made a cohesive set of changes, run the command `git status`.
This will display a list of all the files git has noticed you changed. A file
in the 'untracked' section are files that haven't existed previously in the repository but git has noticed.

To commit changes you have to 'stage' them—this is done by issuing the
following command::
To commit changes you have to 'stage' them—this is done by issuing the following command::

git add path/to/file

Once you have staged your changes, it's time to make a commit::

git commit -m 'Here you provide a brief description of your changes'

Please make your commit message informative but concise - these messages
become part of the 'official' history of the project.
Please make your commit message informative but concise - these messages become part of the 'official' history of the project.

Once your changes have been committed, push them up to the remote branch::

Expand All @@ -224,9 +196,7 @@ Claiming an issue and starting to develop

git pull dib master

(This pulls in all of the latest changes from whatever we've been
doing on dib-lab - important especially during periods of fast change
or for long-running pull requests.)
(This pulls in all of the latest changes from whatever we've been doing on ``dib-lab`` - important especially during periods of fast change or for long-running pull requests.)

#. Run the tests and/or build the docs *before* pushing to GitHub::

Expand All @@ -249,77 +219,59 @@ Claiming an issue and starting to develop

https://github.com/your-github-username/khmer

and you will see a list of "recently pushed branches" just above the
source code listing. On the right side of that should be a
"Compare & pull request" green button. Click on it. This will open up a
submission form with a pull request checklist. In this form:
and you will see a list of "recently pushed branches" just above the source code listing.
On the right side of that should be a "Compare & pull request" green button.
Click on it.
This will open up a submission form with a pull request checklist.
In this form:

* add a descriptive title (e.g. "updated tests for XXX")
* include any relevant comments about your submission in the main body of
the pull request text, above the checklist
* make sure to include any relevant issue numbers in the comments (e.g.
"fixes issue #532")
- add a descriptive title (e.g. "updated tests for XXX")
- include any relevant comments about your submission in the main body of the pull request text, above the checklist
- make sure to include any relevant issue numbers in the comments (e.g. "fixes issue #532")

then click "Create pull request."

(This creates a new issue where we can all discuss your proposed
changes; the khmer team will be automatically notified and you will
receive e-mail notifications as we add comments. See `GitHub flow
<http://scottchacon.com/2011/08/31/github-flow.html>`__ for more
info.)
(This creates a new issue where we can all discuss your proposed changes;
the khmer team will be automatically notified and you will receive e-mail notifications as we add comments.
See `GitHub flow <http://scottchacon.com/2011/08/31/github-flow.html>`__ for more info.)

#. Review the pull request checklist and make any necessary additional changes.

Check off as many of the boxes as you can from the checklist that is
automatically added to the first comment of the Pull Request
discussion. If you have an `ORCID ID<https://orcid.org/>` post that
as well. This will make it much easier for the khmer team to include
you in khmer publications.
Check off as many of the boxes as you can from the checklist that is automatically added to the first comment of the Pull Request discussion.
If you have an `ORCID ID<https://orcid.org/>` post that as well.
This will make it much easier for the khmer team to include you in khmer publications.

As you add new commits to address bugs or formatting issues, you can keep
pushing your changes to the pull request by doing::
As you add new commits to address bugs or formatting issues, you can keep pushing your changes to the pull request by doing::

git push origin

#. When you are ready to have the pull request reviewed, please mention
@luizirber, @camillescott, @standage, @betatim, and/or @ctb with the comment
'Ready for review!'
#. When you are ready to have the pull request reviewed, please mention @luizirber, @camillescott, @standage, @betatim, and/or @ctb with the comment 'Ready for review!'

#. The khmer team will now review your pull request and communicate with you through the pull request page.
Please feel free to add 'ping!' and an @ in the comments if you are looking for feedback—this will alert us that you are still on the line.

#. The khmer team will now review your pull request and communicate
with you through the pull request page. Please feel free to add
'ping!' and an @ in the comments if you are looking for feedback—this
will alert us that you are still on the line.
If this is your first issue, please *don't* take another issue until we've merged your first one. Thanks!

If this is your first issue, please *don't* take another issue until
we've merged your first one. Thanks!
#. If we request changes, return to the step "Make some changes and commit them" and go from there.
Any additional commits you make and push to your branch will automatically be added to the pull request.

#. If we request changes, return to the step "Make some changes and
commit them" and go from there. Any additional commits you make and
push to your branch will automatically be added to the pull request.
After your submission passes peer review and the test suite (``make test`` is run on continuous integration server automatically for each pull request), your contribution will be merged into the main codebase.
Congratulations on making your first contribution to the khmer library!
You're now an experienced GitHub user and an official khmer contributor!

After your submission passes peer review and the test suite (``make test`` is
run on continuous integration server automatically for each pull request), your
contribution will be merged into the main codebase. Congratulations on making
your first contribution to the khmer library! You're now an experienced GitHub
user and an official khmer contributor!

After your first issue is successfully merged...
------------------------------------------------

Before getting started with your second (or third, or fourth, or nth)
contribution, there are a couple of steps you need to take to clean up your
local copy of the code::
Before getting started with your second (or third, or fourth, or nth) contribution, there are a couple of steps you need to take to clean up your local copy of the code::

git checkout master
git pull dib master
git branch -d fix/brief_issue_description # delete the branch locally
git push origin :fix/brief_issue_description # delete the branch on your GitHub fork

This will syncronize your local main (master) branch with the central khmer
repository—including your newly integrated contribution—and delete the branch
you used to make your submission.
This will syncronize your local main (master) branch with the central khmer repository—including your newly integrated contribution—and delete the branch you used to make your submission.

Now your local copy of the code is queued up for another contribution. If you
find another issue that interests you, go back to the beginning of these
instructions and repeat! You will also want to take a look at
:doc:`guidelines-continued-dev`.
Now your local copy of the code is teed up for another contribution.
If you find another issue that interests you, go back to the beginning of these instructions and repeat!
You will also want to take a look at :doc:`guidelines-continued-dev`.

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