From 06a99589a1c5e211f4f1393c73b639e8416cf846 Mon Sep 17 00:00:00 2001 From: Ewan Cahen Date: Mon, 7 Oct 2024 17:30:18 +0200 Subject: [PATCH 1/2] update the Turing Way URLs --- CONTRIBUTING.md | 2 +- README.md | 2 +- best_practices/code_quality.md | 4 ++-- best_practices/documentation.md | 4 ++-- language_guides/python.md | 6 +++--- language_guides/r.md | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 26545a1b..361b91c8 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -53,7 +53,7 @@ The guide contains and links to best practices we use to code and develop resear The main goal: having information available about research software engineering best practices for our colleagues, collaborators and other interested people. It can be information that you can give a colleague starting in some area, for instance, a new language or a new technology. -80% of this goal will be met by [the Turing Way](https://the-turing-way.netlify.app/). +80% of this goal will be met by [the Turing Way](https://book.the-turing-way.org/). For everything else: we have the Guide. We focus on eScience Center-specific best practices. diff --git a/README.md b/README.md index c686d857..0156f1e6 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Center, and as a basis for discussions and reaching consensus on this topic. **Read The Turing Way instead** If you are looking for an overall picture of best practices, read -[The Turing Way](https://the-turing-way.netlify.app/index.html) first. +[The Turing Way](https://book.the-turing-way.org/index.html) first. We joined forces with that guide for most of our generic research software engineering advice. Because The Turing Way is programming language agnostic, this guide provides diff --git a/best_practices/code_quality.md b/best_practices/code_quality.md index e449d9e8..c0000557 100644 --- a/best_practices/code_quality.md +++ b/best_practices/code_quality.md @@ -1,8 +1,8 @@ # Code Quality -Ways to improve code quality are in the [Code quality](https://the-turing-way.netlify.app/reproducible-research/code-quality.html) chapter on the Turing Way. +Ways to improve code quality are in the [Code quality](https://book.the-turing-way.org//reproducible-research/code-quality.html) chapter on the Turing Way. -There are [online software quality improvement tools](https://the-turing-way.netlify.app/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks) see the [language guides](language_guides/languages_overview.md) for good options per language. +There are [online software quality improvement tools](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks) see the [language guides](language_guides/languages_overview.md) for good options per language. ## Editorconfig diff --git a/best_practices/documentation.md b/best_practices/documentation.md index cead8165..dc081701 100644 --- a/best_practices/documentation.md +++ b/best_practices/documentation.md @@ -87,8 +87,8 @@ developer and contributor since things have to be explained only once. A good CO file describes at least how to perform the following tasks: * How to [install the dependencies](#documented-development-setup) -* How to run [(unit) tests](https://the-turing-way.netlify.app/reproducible-research/testing/testing-unittest) -* What [code style](https://the-turing-way.netlify.app/reproducible-research/code-quality/code-quality-style.html) to use +* How to run [(unit) tests](https://book.the-turing-way.org/reproducible-research/testing/testing-unittest) +* What [code style](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-style.html) to use * Reference to [code of conduct](#code-of-conduct) * Mention the [git branching model](https://www.atlassian.com/git/tutorials/comparing-workflows) when using anything else than the [GitHub flow branching model](https://guides.github.com/introduction/flow/) diff --git a/language_guides/python.md b/language_guides/python.md index 026f79e6..87454562 100644 --- a/language_guides/python.md +++ b/language_guides/python.md @@ -189,7 +189,7 @@ The development environment will typically accumulate (old) packages during deve ### Code coverage When you have tests it is also a good to see which source code is exercised by the test suite. -[Code coverage](https://the-turing-way.netlify.app/reproducible-research/testing/testing-guidance#aim-to-have-a-good-code-coverage) can be measured with the [coverage](https://coverage.readthedocs.io) Python package. +[Code coverage](https://book.the-turing-way.org/reproducible-research/testing/testing-guidance#aim-to-have-a-good-code-coverage) can be measured with the [coverage](https://coverage.readthedocs.io) Python package. The coverage package can also generate html reports which show which line was covered. Most test runners have have the coverage package integrated. @@ -199,9 +199,9 @@ If this is not possible or does not fit then use a generic code coverage service ## Code quality analysis tools and services -Code quality service is explained in the [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks). +Code quality service is explained in the [The Turing Way](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks). There are multiple code quality services available for Python, all of which have their pros and cons. -See [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/code-quality/code-quality-resources.html) for links to lists of possible services. +See [The Turing Way](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-resources.html) for links to lists of possible services. We currently setup [Sonarcloud](https://sonarcloud.io/) by default in our [Python template](https://github.com/NLeSC/python-template). To reproduce the Sonarcloud pipeline locally, you can use [SonarLint](https://www.sonarlint.org/) in your IDE. If you use another editor, perhaps it is more convenient to pick another service like Codacy or Codecov. diff --git a/language_guides/r.md b/language_guides/r.md index c84d3f1d..917c4ca3 100644 --- a/language_guides/r.md +++ b/language_guides/r.md @@ -127,7 +127,7 @@ R function documentation offers plenty of space to document the functionality, i See also [checking](http://r-pkgs.had.co.nz/check.html) and [testing](http://r-pkgs.had.co.nz/tests.html) R packages. note that within RStudio R package check and R package test can be done via simple toolbar clicks. ### Continuous integration -[Continuous integration](https://the-turing-way.netlify.app/reproducible-research/ci) should be done with an online service. +[Continuous integration](https://book.the-turing-way.org/reproducible-research/ci) should be done with an online service. ### Debugging and Profiling Debugging is possible in RStudio, see [link](https://support.posit.co/hc/en-us/articles/205612627-Debugging-with-RStudio). For profiling tips see [link](http://adv-r.had.co.nz/Profiling.html) From 5eb361c5ab1b39ce5e9e0e97121122f836930480 Mon Sep 17 00:00:00 2001 From: Ewan Cahen Date: Mon, 7 Oct 2024 17:42:48 +0200 Subject: [PATCH 2/2] fix broken links to language guide --- best_practices/code_quality.md | 2 +- best_practices/overview.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/best_practices/code_quality.md b/best_practices/code_quality.md index c0000557..ea9bb01c 100644 --- a/best_practices/code_quality.md +++ b/best_practices/code_quality.md @@ -2,7 +2,7 @@ Ways to improve code quality are in the [Code quality](https://book.the-turing-way.org//reproducible-research/code-quality.html) chapter on the Turing Way. -There are [online software quality improvement tools](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks) see the [language guides](language_guides/languages_overview.md) for good options per language. +There are [online software quality improvement tools](https://book.the-turing-way.org/reproducible-research/code-quality/code-quality-style.html#online-services-providing-software-quality-checks) see the [language guides](/language_guides/languages_overview.md) for good options per language. ## Editorconfig diff --git a/best_practices/overview.md b/best_practices/overview.md index 54e70ba3..8f6d512f 100644 --- a/best_practices/overview.md +++ b/best_practices/overview.md @@ -10,7 +10,7 @@ things done faster. ### Learn how to use the command line efficiently -Read the chapter on using [Bash](language_guides/bash.md). +Read the chapter on using [Bash](/language_guides/bash.md). ### Use an editor that helps you develop