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How to contribute to Lisp-Stat
This section describes the mechanics of how to contribute code to
Lisp-Stat. Legal requirements, community guidelines, code of
conduct, etc. For details on how to contribute code and documentation,
see links on nav sidebar to the left under Contributing.
For ideas about what you might contribute, please see
open issues on github and the ideas page. The
organisation repository contains the
individual sub-projects. Contributions to
Contributor License Agreement
Contributor License Agreements (CLAs) are common and accepted in open
source projects. We all wish for Lisp-Stat to be used and distributed
as widely as possible, and for its users to be confident about the
origins and continuing existence of the code. The CLA help us achieve
that goal. Although common, many in the Lisp community are unaware of
CLAs or their importance.
Some often asked questions include:
Why do you need a CLA?
We need a CLA because, by law, all rights reside with the originator
of a work unless otherwise agreed. The CLA allows the project to
accept and distribute your contributions. Without your consent via a
CLA, the project has no rights to use the code. Here’s what Google has
to say in their CLA policy page:
Standard inbound license
Using one standard inbound license that grants the receiving company broad permission to use contributed code in products is beneficial to the company and downstream users alike.
Technology companies will naturally want to make productive use of any code made available to them. However, if all of the code being received by a company was subject to various inbound licenses with conflicting terms, the process for authorizing the use of the code would be cumbersome because of the need for constant checks for compliance with the various licenses. Whenever contributed code were to be used, the particular license terms for every single file would need to be reviewed to ascertain whether the application would be permitted under the terms of that code’s specific license. This would require considerable human resources and would slow down the engineers trying to utilize the code.
The benefits that a company receives under a standard inbound license pass to downstream users as well. Explicit patent permissions and disclaimers of obligations and warranties clarify the recipients’ rights and duties. The broad grant of rights provides code recipients opportunities to make productive use of the software. Adherence to a single standard license promotes consistency and common understanding for all parties involved.
How do I sign?
In order to be legally binding a certain amount of legal ceremony must
take place. This varies by jurisdiction. As an individual
‘clickwrap’ or ‘browser
wrap’ agreements are used.
For corporations, a ‘wet signature’ is required because it is valid
everywhere and avoids ambiguity of assent.
If you are an individual contributor, making a pull request from a
personal account, the cla-assistant will
automatically prompt you to digitally sign as part of the PR.
What does it do?
The CLA essentially does three things. It ensures that the contributor agrees:
- To allow the project to use the source code and redistribute it
- The contribution is theirs to give, e.g. does not belong to their employer or someone else
- Does not contain any patented ‘stuff’.
Mechanics of the CLA
The Lisp-Stat project uses CLAs to accept regular contributions from
individuals and corporations, and to accept larger grants of existing
software products, for example if you wished to contribute a large
Contributions to this project must be accompanied by a Contributor
License Agreement. You (or your employer) retain the copyright to your
contribution; this simply gives us permission to use and redistribute
your contributions as part of the project.
You generally only need to submit a CLA once, so if you have already
submitted one (even if it was for a different project), you do not
need to do it again.
Code of Conduct
The following code of conduct is not meant as a means for punishment,
action or censorship for the mailing list or project. Instead, it is
meant to set the tone, expectations and comfort level for contributors
and those wishing to participate in the community.
- We ask everyone to be welcoming, friendly, and patient.
- Flame wars and insults are unacceptable in any fashion, by any party.
- Anything can be asked, and “RTFM” is not an acceptable answer.
- Neither is “it’s in the archives, go read them”.
- Statements made by core developers can be quoted outside of the list.
- Statements made by others can not be quoted outside the list without explicit permission. - Anonymised paraphrased statements “someone asked about…” are OK - direct quotes with or without names are not appropriate.
- The community administrators reserve the right to revoke the subscription of members (including mentors) that persistently fail to abide by this Code of Conduct.
1 - Contributing Code
How to contribute code to Lisp-Stat
First, if you are contributing on behalf of your employer, ensure you
have signed a contributor license
follow these steps for contributing to Lisp-Stat:
You may also be interested in the additional
information at the end of this document.
Get source code
First you need the Lisp-Stat source code. The core systems are found
on the Lisp-Stat github page. For the
individual systems, just check out the one you are interested in. For
the entire Lisp-Stat system, at a minimum you will need:
Other dependencies will be pulled in by Quicklisp.
Development occurs on the “master” branch. To get all the repos, you
can use the following command in the directory you want to be your top
level dev space:
git clone https://github.com/Lisp-Stat/data-frame.git && \
git clone https://github.com/Lisp-Stat/dfio.git && \
git clone https://github.com/Lisp-Stat/special-functions.git && \
git clone https://github.com/Lisp-Stat/numerical-utilities.git && \
git clone https://github.com/Lisp-Stat/documentation.git && \
git clone https://github.com/Lisp-Stat/lisp-stat.git && \
git clone https://github.com/Lisp-Stat/plot.git && \
git clone https://github.com/Lisp-Stat/select.git && \
git clone https://github.com/Lisp-Stat/array-operations.git && \
git clone https://github.com/Lisp-Stat/sqldf.git
Modify the source
Before you start, send a message to the Lisp-Stat mailing
list or file an issue on
Github describing your proposed changes. Doing this helps to verify
that your changes will work with what others are doing and have
planned for the project. Importantly, there may be some existing code
or design work for you to leverage that is not yet published, and we’d
hate to see work duplicated unnecessarily.
Be patient, it may take folks a while to understand your
requirements. For large systems or design changes, a design document
is preferred. For small changes, issues and the mailing list are fine.
Once your suggested changes are agreed, you can modify the source code
and add some features using your favorite IDE.
The following sections provide tips for working on the project:
Please consider the following before submitting a pull request:
- Code should be formatted according to the Google Common Lisp Style Guide
- All code should include unit tests. Older projects use fiveam as the test framework for new projects. New project should use Parachute.
- Contributions should pass existing unit tests
- New unit tests should be provided to demonstrate bugs and fixes
- Indentation in Common Lisp is important for readability. Contributions should adhere to these guidelines. For the most part, a properly configured Emacs will do this automatically.
Github includes code review
tools that can be used as
part of a pull request. We recommend using a triangular
feature/bug branches in your own repository to work from. Once you
submit a pull request, one of the committers will review it and
possibly request modifications.
As a contributor you should organise
git commits to make them understandable to reviewers:
- Combine WIP and other small commits together.
- Address multiple issues, for smaller bug fixes or enhancements, with a single commit.
- Use separate commits to allow efficient review, separating out formatting changes or simple refactoring from core changes or additions.
- Rebase this chain of commits on top of the current master
- Write a good git commit message
Once all the comments in the review have been addressed, a Lisp-Stat committer completes the following steps to commit the patch:
- If the master branch has moved forward since the review, rebase the branch from the pull request on the latest master and re-run tests.
- If all tests pass, the committer amends the last commit message in the series to include “this closes #1234”. This can be done with interactive rebase. When on the branch issue:
git rebase -i HEAD^
- Change where it says “pick” on the line with the last commit, replacing it with “r” or “reword”. It replays the commit giving you the opportunity the change the commit message.
- The committer pushes the commit(s) to the github repo
- The committer resolves the issue with a message like
"Fixed in <Git commit SHA>".
Where to start?
If you are new to statistics or Lisp, documentation updates are always
a good place to start. You will become familiar with the workflow,
learn how the code functions and generally become better acquainted
with how Lisp-Stat operates. Besides, any contribution will require
documentation updates, so it’s good to learn this system first.
If you are coming from an existing statistical environment, consider
porting a XLispStat package that you find useful to Lisp-Stat. Use
the XLS compatibility layer to
help. If there is a function missing in XLS, raise an issue and we’ll
create it. Some XLispStat code to browse:
Keep in mind that some of these rely on the XLispStat graphics
system, which was native to the platform. LISP-STAT uses Vega for
visualizations, so there isn’t a direct mapping. Non-graphical code
should be a straight forward port.
You could also look at CRAN, which
contains thousands of high-quality packages.
For specific ideas that would help, see the
Please comment on issues in github, making your concerns known. Please
also vote for issues that are a high priority for you.
Please refrain from editing descriptions and comments if possible, as
edits spam the mailing list and clutter the audit trails, which is
otherwise very useful. Instead, preview descriptions and comments
using the preview button (on the right) before posting them. Keep
descriptions brief and save more elaborate proposals for comments,
since descriptions are included in GitHub automatically sent
messages. If you change your mind, note this in a new comment, rather
than editing an older comment. The issue should preserve this history
of the discussion.
2 - Contributing to Documentation
You can help make Lisp-Stat documentation better
Creating and updating documentation is a great way to learn. You will
not only become more familiar with Common Lisp, you have a chance to
investigate the internals of all parts of a statistical system.
We use Hugo to format and generate the website,
the Docsy theme for styling and
site structure, and Netlify to manage the
deployment of the documentation site (what you are reading now). Hugo
is an open-source static site generator that provides us with
templates, content organisation in a standard directory structure, and
a website generation engine. You write the pages in Markdown (or HTML
if you want), and Hugo wraps them up into a website.
All submissions, including submissions by project members, require review. We
use GitHub pull requests for this purpose. Consult
GitHub Help for more
information on using pull requests.
Declt generates documentation for individual systems in Markdown
format. These are kept with the project, e.g.
Please follow the Microsoft Style
Here’s a quick guide to updating the docs. It assumes you are familiar
with the GitHub workflow and you are happy to use the automated preview
of your doc updates:
- Fork the Lisp-Stat documentation repo on GitHub.
- Make your changes and send a pull request (PR).
- If you are not yet ready for a review, add “WIP” to the PR name to indicate
it’s a work in progress. (Don’t add the Hugo property
“draft = true” to the page front matter, because that prevents the
auto-deployment of the content preview described in the next point.)
- Wait for the automated PR workflow to do some checks. When it’s ready,
you should see a comment like this: deploy/netlify — Deploy preview ready!
- Click Details to the right of “Deploy preview ready” to see a preview
of your updates.
- Continue updating your doc and pushing your changes until you’re happy with
- When you’re ready for a review, add a comment to the PR, and remove any
Updating a single page
If you’ve just spotted something you’d like to change while using the
docs, Docsy has a shortcut for you (do not use this for reference
- Click Edit this page in the top right hand corner of the page.
- If you don’t already have an up to date fork of the project repo, you are prompted to get one - click Fork this repository and propose changes or Update your Fork to get an up to date version of the project to edit. The appropriate page in your fork is displayed in edit mode.
- Follow the rest of the Quick Start process above to make, preview, and propose your changes.
If you want to run your own local Hugo server to preview your changes as you work:
Follow the instructions in Getting started to install Hugo and any other tools you need. You’ll need at least Hugo version 0.45 (we recommend using the most recent available version), and it must be the extended version, which supports SCSS.
Fork the Lisp-Stat documentation repo into your own repository project, then create a local copy using
git clone. Don’t forget to use
--recurse-submodules or you won’t pull down some of the code you need to generate a working site.
git clone --recurse-submodules --depth 1 https://github.com/lisp-stat/documentation.git
hugo server in the site root directory. By default your site will be available at http://localhost:1313/. Now that you’re serving your site locally, Hugo will watch for changes to the content and automatically refresh your site.
Continue with the usual GitHub workflow to edit files, commit them, push the
changes up to your fork, and create a pull request.
Creating an issue
If you’ve found a problem in the docs, but are not sure how to fix it
yourself, please create an issue in the Lisp-Stat documentation
repo. You can
also create an issue about a specific page by clicking the Create
Issue button in the top right hand corner of the page.
3 - Contribution Ideas
Some ideas on how contribute to Lisp-Stat
The functions underlying the statistical distributions require skills
in numerical programming. If you like being ‘close to the metal’, this
is a good area for contributions. Suitable for medium-advanced level
programmers. In particular we need implementations of:
- incomplete gamma (upper & lower)
- inverse incomplete gamma
This work is partially complete and makes a good starting point for
someone who wants to make a substantial contribution.
Better and more documentation is always welcome, and a great way to
learn. Suitable for beginners to Common Lisp or statistics.
Jupyter Lab has two nice integrations with Pandas, the Python version
of Data-Frame, that would make great contributions:
Qgrid, which allows editing a
data frame in Jupyter Lab, and Jupyter
DataTables. There are
many more Pandas/Jupyter integrations, and any of them would be
welcome additions to the Lisp-Stat ecosystem.
LISP-STAT has a basic plotting system, but there is always room for
improvement. An interactive REPL based plotting system should be
possible with a medium amount of
effort. Remote-js provides a
could combined with something like Electron and a DSL for Vega-lite
specifications. This may be a 4-6 week project for someone with
if this interests you, open an issue and we can discuss. I have
working examples of much of this, but all fragmented examples. Skills:
We have some code for ‘quick & dirty’ regressions and need a more
robust DSL (Domain Specific Language). As a prototype, the -proto
regression objects from XLISP-STAT would be both useful and be a good
experiment to see what the final form should take. This is a
relatively straightforward port, e.g.
defproto -> defclass and
defmeth -> defmethod. Skill level: medium in both Lisp and
statistics, or willing to learn.
We have code for vectorized versions of all Common Lisp functions,
living in the
elmt package. It now only works on vectors. Shadowing
Common Lisp mathematical operators is possible, and more natural. This
task is to make
elmt vectorized math functions work on lists as well
as vectors, and to implement shadowing of Common Lisp. This task
requires at least medium-high level Lisp skills, since you will be
working with both packages and shadowing. We also need to run the
ANSI Common Lisp conformance tests on the results to ensure nothing
gets broken in the process.
If you have experience with Github’s CI tools, a CI setup for
Lisp-Stat would be a great help. This allows people making pull
requests to immediately know if their patches break anything. Beginner