From e59b91ccbc29a619af938456cc48beb7bc854339 Mon Sep 17 00:00:00 2001 From: katiebuntic Date: Tue, 24 Oct 2023 11:14:54 +0100 Subject: [PATCH 01/12] adding used by to all tables --- docs/pages/benchmarking.md | 16 ++++++++-------- docs/pages/bindings.md | 14 +++++++------- docs/pages/ci.md | 20 ++++++++++---------- docs/pages/dev.md | 34 +++++++++++++++++----------------- docs/pages/linting.md | 28 ++++++++++++++-------------- docs/pages/packaging.md | 14 +++++++------- docs/pages/templates.md | 14 +++++++------- docs/pages/testing.md | 18 +++++++++--------- 8 files changed, 79 insertions(+), 79 deletions(-) diff --git a/docs/pages/benchmarking.md b/docs/pages/benchmarking.md index 85fac229..41d08848 100644 --- a/docs/pages/benchmarking.md +++ b/docs/pages/benchmarking.md @@ -5,11 +5,11 @@ layout: default # Benchmarking -| Name | Short description | 🚦 | -| ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-: | -| [pyinstrument](https://pyinstrument.readthedocs.io/en/stable) | Python profiler. Tells you how long individual lines of code take to run, so you can focus on the slowest part of your program to speed it up. | 🟒 | -| [snakeviz](https://jiffyclub.github.io/snakeviz/) | Browser based graphical viewer for the output of Python’s cProfile module. | 🟒 | -| [asv](https://asv.readthedocs.io/en/stable/) | A tool for benchmarking Python packages over their lifetime. Allows you to write benchmarks and then run them against every commit in the repository, to identify where performance increased or decreased. | 🟒 | -| [memray](https://bloomberg.github.io/memray/) | Memray tracks and reports memory allocations, both in Python code and in compiled extension modules. It also has a [plugin](https://pytest-memray.readthedocs.io/en/latest/) for easy integration with pytest. However, it only works on Linux and MacOS, and cannot be installed on other platforms. | 🟠 | -| [line_profiler](https://pypi.org/project/line-profiler/) | It is a module for doing line-by-line profiling of functions. | 🟠 | -| [memory_profiler](https://pypi.org/project/memory-profiler/) | This package is no longer actively maintained. It is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption. | πŸ”΄ | +| Name | Short description | 🚦 | Used by | +| ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------| :-: | +| [pyinstrument](https://pyinstrument.readthedocs.io/en/stable) | Python profiler. Tells you how long individual lines of code take to run, so you can focus on the slowest part of your program to speed it up. | 🟒 | | +| [snakeviz](https://jiffyclub.github.io/snakeviz/) | Browser based graphical viewer for the output of Python’s cProfile module. | 🟒 | | +| [asv](https://asv.readthedocs.io/en/stable/) | A tool for benchmarking Python packages over their lifetime. Allows you to write benchmarks and then run them against every commit in the repository, to identify where performance increased or decreased. | 🟒 | | +| [memray](https://bloomberg.github.io/memray/) | Memray tracks and reports memory allocations, both in Python code and in compiled extension modules. It also has a [plugin](https://pytest-memray.readthedocs.io/en/latest/) for easy integration with pytest. However, it only works on Linux and MacOS, and cannot be installed on other platforms. | 🟠 | | +| [line_profiler](https://pypi.org/project/line-profiler/) | It is a module for doing line-by-line profiling of functions. | 🟠 | | +| [memory_profiler](https://pypi.org/project/memory-profiler/) | This package is no longer actively maintained. It is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption. | πŸ”΄ | | diff --git a/docs/pages/bindings.md b/docs/pages/bindings.md index 1b7ddc65..d16ad205 100644 --- a/docs/pages/bindings.md +++ b/docs/pages/bindings.md @@ -5,10 +5,10 @@ layout: default # Bindings -| Name | Short description | 🚦 | -| --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | :-: | -| [Cython](https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html) | C/C++ binding library with numpy array integration | 🟒 | -| [ctypes](https://docs.python.org/3.8/library/ctypes.html) | Native python method for calling functions in shared C libraries | 🟠 | -| [pybind11](https://github.com/pybind/pybind11) | Bindings to C++ with a steep learning curve | 🟠 | -| [f2py](https://numpy.org/devdocs/f2py/f2py.getting-started.html) | Bindings to Fortran developed by numpy | 🟠 | -| [pyO3](https://github.com/PyO3/pyo3) | Straightforward bindings to rust with support for [packaging](https://github.com/PyO3/maturin) | 🟒 | +| Name | Short description | 🚦 | Used by | +| --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | ----| :-: | +| [Cython](https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html) | C/C++ binding library with numpy array integration | 🟒 | | +| [ctypes](https://docs.python.org/3.8/library/ctypes.html) | Native python method for calling functions in shared C libraries | 🟠 | | +| [pybind11](https://github.com/pybind/pybind11) | Bindings to C++ with a steep learning curve | 🟠 | | +| [f2py](https://numpy.org/devdocs/f2py/f2py.getting-started.html) | Bindings to Fortran developed by numpy | 🟠 | | +| [pyO3](https://github.com/PyO3/pyo3) | Straightforward bindings to rust with support for [packaging](https://github.com/PyO3/maturin) | 🟒 | | diff --git a/docs/pages/ci.md b/docs/pages/ci.md index f6fd505f..cf8b318b 100644 --- a/docs/pages/ci.md +++ b/docs/pages/ci.md @@ -5,12 +5,12 @@ layout: default # Continuous integration -| Name | Short description | 🚦 | -| ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | :-: | -| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | -| [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | -| [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | -| [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | +| Name | Short description | 🚦 | Used by | +| ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-: | +| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | | +| [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | +| [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | +| [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | |
🟒 explanation @@ -19,7 +19,7 @@ We have many projects using github CI, it's both convenient and works well. It's # Coverage monitoring -| Name | Short description | 🚦 | -| ---------------------------------------- | ----------------------------------------------- | :-: | -| [Codecov](https://docs.codecov.com/docs) | Hosted service to report code coverage metrics. | 🟒 | -| [Coveralls](https://docs.coveralls.io/) | Hosted service to report code coverage metrics. | 🟠 | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------- | ----------------------------------------------- | ---- | :-: | +| [Codecov](https://docs.codecov.com/docs) | Hosted service to report code coverage metrics. | 🟒 | | +| [Coveralls](https://docs.coveralls.io/) | Hosted service to report code coverage metrics. | 🟠 | | diff --git a/docs/pages/dev.md b/docs/pages/dev.md index 0eb064ea..cbdb0667 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -6,26 +6,26 @@ layout: default # Integrated Development Environments (IDEs) | Name | Short description | 🚦 | -| -------------------------------------------------------- | ----------------------------------- | :-: | -| [Visual Studio Code](https://code.visualstudio.com/docs) | A light-weight general-purpose IDE. | 🟠 | -| [PyCharm](https://www.jetbrains.com/pycharm/) | A Python IDE by JetBrains. | 🟠 | +| -------------------------------------------------------- | ----------------------------------- | ---- | :-: | +| [Visual Studio Code](https://code.visualstudio.com/docs) | A light-weight general-purpose IDE. | 🟠 | | +| [PyCharm](https://www.jetbrains.com/pycharm/) | A Python IDE by JetBrains. | 🟠 | | # Virtual environments -| Name | Short description | 🚦 | -| --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | :-: | -| [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) | A tool to manage conda environments. Faster than conda for installing dependencies. | 🟒 | -| [conda](https://conda.io/projects/conda/en/latest/) | Conda quickly installs, runs, and updates packages and their dependencies. | 🟠 | -| [pipenv](https://pipenv.pypa.io/en/latest/) | A tool that automatically creates and manages a virtualenv for your projects. | 🟠 | -| [venv](https://docs.python.org/3/library/venv.html) | A tool to create isolated Python environments. | πŸ”΄ | -| [virtualenv](https://virtualenv.pypa.io/en/latest/) | A tool to create isolated Python environments which offers more features than venv. | 🟠 | -| [pyenv](https://github.com/pyenv/pyenv) | A tool that lets you easily switch between multiple versions of Python. | 🟠 | +| Name | Short description | 🚦 | Used by | +| --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | ---- | :-: | +| [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) | A tool to manage conda environments. Faster than conda for installing dependencies. | 🟒 | | +| [conda](https://conda.io/projects/conda/en/latest/) | Conda quickly installs, runs, and updates packages and their dependencies. | 🟠 | | +| [pipenv](https://pipenv.pypa.io/en/latest/) | A tool that automatically creates and manages a virtualenv for your projects. | 🟠 | | +| [venv](https://docs.python.org/3/library/venv.html) | A tool to create isolated Python environments. | πŸ”΄ | | +| [virtualenv](https://virtualenv.pypa.io/en/latest/) | A tool to create isolated Python environments which offers more features than venv. | 🟠 | | +| [pyenv](https://github.com/pyenv/pyenv) | A tool that lets you easily switch between multiple versions of Python. | 🟠 | | # Other -| Name | Short description | 🚦 | -| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | :-: | -| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | | -| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | -| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | | -| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-: | +| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | | | +| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | +| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | | | +| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | | | diff --git a/docs/pages/linting.md b/docs/pages/linting.md index 0968b7cd..d6b437a2 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -9,20 +9,20 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b ## Code formatting -| Name | Short description | 🚦 | -| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-: | -| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | -| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | -| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | -| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | -| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | -| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | -| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | -| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | -| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | -| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | +| Name | Short description | 🚦 | Used by | +| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---- | :-: | +| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | | +| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | | +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | | +| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | +| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | +| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | +| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | | +| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | | +| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | | +| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | | +| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | |
🟒 explaination diff --git a/docs/pages/packaging.md b/docs/pages/packaging.md index 130ffa16..479f7b7f 100644 --- a/docs/pages/packaging.md +++ b/docs/pages/packaging.md @@ -5,17 +5,17 @@ layout: default # Packaging -| Name | Short description | Used by | 🚦 | +| Name | Short description | 🚦 | Used by | | --------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------- | :-: | -| [build](https://pypa-build.readthedocs.io/en/stable/) | Straightforward tool to build a Python package. | | 🟒 | -| [setuptools](https://setuptools.pypa.io) | A widely used build backend, used to configure a Python package. | [autodE](https://github.com/duartegroup/autodE) | 🟒 | -| [setuptools-scm](https://github.com/pypa/setuptools_scm/) | Provides automatic versioning Python packages. Also automatically adds all files under source control to the sdist / wheel. | [btrack](https://github.com/quantumjot/btrack) | 🟒 | -| [cibuildwheel](https://cibuildwheel.readthedocs.io) | Builds python wheels for the main operating systems on continuous integration runs (e.g. GitHub actions). | [streamtracer](https://github.com/dstansby/streamtracer) | 🟒 | +| [build](https://pypa-build.readthedocs.io/en/stable/) | Straightforward tool to build a Python package. | 🟒 | | +| [setuptools](https://setuptools.pypa.io) | A widely used build backend, used to configure a Python package. | 🟒 | [autodE](https://github.com/duartegroup/autodE) | +| [setuptools-scm](https://github.com/pypa/setuptools_scm/) | Provides automatic versioning Python packages. Also automatically adds all files under source control to the sdist / wheel. | 🟒 | [btrack](https://github.com/quantumjot/btrack) | +| [cibuildwheel](https://cibuildwheel.readthedocs.io) | Builds python wheels for the main operating systems on continuous integration runs (e.g. GitHub actions). | 🟒 | [streamtracer](https://github.com/dstansby/streamtracer) | ## Conda These tools are helpful if you're looking to publish your package on [conda-forge](https://conda-forge.org/), so users can install it through the [conda](https://docs.conda.io/en/latest/) or [mamba](https://mamba.readthedocs.io/en/latest/index.html) package managers. -| Name | Short description | Used by | 🚦 | +| Name | Short description | 🚦 | Used by | | --------------------------------------------------------- | --------------------------------------------------------------------------- | ------- | :-: | -| [GraySkull](https://github.com/conda-incubator/grayskull) | A tool for automatic conda recipe generation (aimed at conda-forge, above). | | 🟒 | +| [GraySkull](https://github.com/conda-incubator/grayskull) | A tool for automatic conda recipe generation (aimed at conda-forge, above). | 🟒 | | diff --git a/docs/pages/templates.md b/docs/pages/templates.md index d83b1556..2cb5a060 100644 --- a/docs/pages/templates.md +++ b/docs/pages/templates.md @@ -29,10 +29,10 @@ If you're making a package within one of these communities, we recommend using t These are packages that can be used for creating your own package template. -| Name | Short description | 🚦 | -| ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | :-: | -| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates, but is not maintained. | πŸ”΄ | -| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is actively maintained. | 🟒 | -| [Cruft](https://github.com/cruft/cruft) | Can be used to create projects from a cookiecutter template and to keep the project configuration in sync with the template. | 🟠 | -| [Copier](https://github.com/copier-org/copier) | A tool to create project templates that are highly configurable. Project configuration can be kept in sync with the templae. | 🟠 | -| [GitHub templates](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) | GitHub repositories can be used as templates, but they are not configurable. | 🟠 | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | ----- | :-: | +| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates, but is not maintained. | πŸ”΄ | | +| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is actively maintained. | 🟒 | | +| [Cruft](https://github.com/cruft/cruft) | Can be used to create projects from a cookiecutter template and to keep the project configuration in sync with the template. | 🟠 | | +| [Copier](https://github.com/copier-org/copier) | A tool to create project templates that are highly configurable. Project configuration can be kept in sync with the templae. | 🟠 | | +| [GitHub templates](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) | GitHub repositories can be used as templates, but they are not configurable. | 🟠 | | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 8cc5dcce..72a5e9da 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -7,11 +7,11 @@ layout: default ## Test runners -| Name | Short description | 🚦 | -| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | :-: | -| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | -| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | -| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | ---- | :-: | +| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | | +| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | | +| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
🟒 explanation @@ -20,7 +20,7 @@ We recommend `pytest` over `unittest` because `pytest` tends to encourage a clea ## pytest plugins -| Name | Short description | 🚦 | -| ---------------------------------------------------------------------- | ------------------------------------------------------------------------- | :-: | -| [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/index.html) | A framework to generate coverage reports that plays nicely with `pytest`. | 🟒 | -| [pytest-mock](https://pytest-mock.readthedocs.io/en/latest/index.html) | A framework to mock/patch objects that plays nicely with `pytest`. | 🟒 | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------------------------------------- | ------------------------------------------------------------------------- | ---- | :-: | +| [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/index.html) | A framework to generate coverage reports that plays nicely with `pytest`. | 🟒 | | +| [pytest-mock](https://pytest-mock.readthedocs.io/en/latest/index.html) | A framework to mock/patch objects that plays nicely with `pytest`. | 🟒 | | From aa469fe3b2c88df0733dfd832ce08ef3a54db055 Mon Sep 17 00:00:00 2001 From: katiebuntic Date: Tue, 24 Oct 2023 11:38:15 +0100 Subject: [PATCH 02/12] adding in projects --- docs/pages/ci.md | 2 +- docs/pages/linting.md | 12 ++++++------ docs/pages/testing.md | 8 ++++---- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/pages/ci.md b/docs/pages/ci.md index cf8b318b..ab85480d 100644 --- a/docs/pages/ci.md +++ b/docs/pages/ci.md @@ -7,7 +7,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-: | -| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | | +| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | | [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | | [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | | [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | | diff --git a/docs/pages/linting.md b/docs/pages/linting.md index d6b437a2..9c6f4957 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -11,10 +11,10 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b | Name | Short description | 🚦 | Used by | | -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---- | :-: | -| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | | +| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | | [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | | -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | | +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | | [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | | [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | | [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | @@ -44,6 +44,6 @@ Flake8 is not recommended because it doesn't support `pyproject.toml` and [seemi ## Type checking -| Name | Short description | 🚦 | -| ---------------------------------------------- | ----------------------------------------------------------------------------- | :-: | -| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------------- | ----------------------------------------------------------------------------- | ----- | :-: | +| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 72a5e9da..1614b6c3 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -9,8 +9,8 @@ layout: default | Name | Short description | 🚦 | Used by | | ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | ---- | :-: | -| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | | -| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | | +| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | +| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | | [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
@@ -22,5 +22,5 @@ We recommend `pytest` over `unittest` because `pytest` tends to encourage a clea | Name | Short description | 🚦 | Used by | | ---------------------------------------------------------------------- | ------------------------------------------------------------------------- | ---- | :-: | -| [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/index.html) | A framework to generate coverage reports that plays nicely with `pytest`. | 🟒 | | -| [pytest-mock](https://pytest-mock.readthedocs.io/en/latest/index.html) | A framework to mock/patch objects that plays nicely with `pytest`. | 🟒 | | +| [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/index.html) | A framework to generate coverage reports that plays nicely with `pytest`. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | +| [pytest-mock](https://pytest-mock.readthedocs.io/en/latest/index.html) | A framework to mock/patch objects that plays nicely with `pytest`. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | From afe765fac1e7e9ed7193b90d1b77bbeb8feba3ac Mon Sep 17 00:00:00 2001 From: katiebuntic Date: Tue, 24 Oct 2023 12:00:01 +0100 Subject: [PATCH 03/12] adding projects to used by --- docs/pages/ci.md | 2 +- docs/pages/dev.md | 2 +- docs/pages/docs.md | 2 +- docs/pages/linting.md | 10 +++++----- docs/pages/testing.md | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/pages/ci.md b/docs/pages/ci.md index ab85480d..39eaf286 100644 --- a/docs/pages/ci.md +++ b/docs/pages/ci.md @@ -7,7 +7,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-: | -| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED](https://github.com/UCL-ARC/rred-reports) | | [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | | [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | | [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | | diff --git a/docs/pages/dev.md b/docs/pages/dev.md index cbdb0667..c6d97391 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -5,7 +5,7 @@ layout: default # Integrated Development Environments (IDEs) -| Name | Short description | 🚦 | +| Name | Short description | 🚦 | Used by | | -------------------------------------------------------- | ----------------------------------- | ---- | :-: | | [Visual Studio Code](https://code.visualstudio.com/docs) | A light-weight general-purpose IDE. | 🟠 | | | [PyCharm](https://www.jetbrains.com/pycharm/) | A Python IDE by JetBrains. | 🟠 | | diff --git a/docs/pages/docs.md b/docs/pages/docs.md index 7ec796cc..58878e56 100644 --- a/docs/pages/docs.md +++ b/docs/pages/docs.md @@ -10,7 +10,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ----------------------------------------------- | --------------------------------------------------------------- | :-: | ---------------------------------------------------------------------- | | [sphinx](https://www.sphinx-doc.org/en/master/) | Generates documentation from reStructuredText or Markdown files | 🟒 | [WAZP](https://github.com/SainsburyWellcomeCentre/WAZP/tree/main/docs) | -| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | | +| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | | [pdoc](https://pdoc.dev/) | Auto-generates API documentation from docstrings | 🟠 | [MICI](https://github.com/matt-graham/mici) | | [gitbook](https://www.gitbook.com/) | General documentation builder; integrates with GitHub | 🟠 | | diff --git a/docs/pages/linting.md b/docs/pages/linting.md index 9c6f4957..33b0836a 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -11,10 +11,10 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b | Name | Short description | 🚦 | Used by | | -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---- | :-: | -| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | -| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | | -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | +| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi)| +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi)| | [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | | [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | | [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | @@ -46,4 +46,4 @@ Flake8 is not recommended because it doesn't support `pyproject.toml` and [seemi | Name | Short description | 🚦 | Used by | | ---------------------------------------------- | ----------------------------------------------------------------------------- | ----- | :-: | -| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 1614b6c3..635183ef 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -10,7 +10,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | ---- | :-: | | [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | -| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
From aa45335402534da9ae8e18915d7cf07f80994ee1 Mon Sep 17 00:00:00 2001 From: katiebuntic Date: Tue, 24 Oct 2023 12:16:43 +0100 Subject: [PATCH 04/12] adding projects to dev --- docs/pages/dev.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/pages/dev.md b/docs/pages/dev.md index c6d97391..b5314627 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -25,7 +25,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-: | -| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | | | +| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | | [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | -| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | | | +| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | | [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | | | From 7390d7e76f069f7cecd13b70209109bbd7300f0b Mon Sep 17 00:00:00 2001 From: katiebuntic Date: Tue, 24 Oct 2023 12:26:16 +0100 Subject: [PATCH 05/12] adding to dev --- docs/pages/dev.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pages/dev.md b/docs/pages/dev.md index b5314627..8b0dfd4b 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -28,4 +28,4 @@ layout: default | [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | | [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | | [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | | | +| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer,](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) [Puppet Submitty,](https://github.com/UCL-ARC/puppet-submitty) [Quality Workflow tool](https://github.com/UCL-ARC/qw) | From 0b7cebc8a184aa535bff00df411a702e081df49a Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Tue, 24 Oct 2023 16:28:11 +0100 Subject: [PATCH 06/12] Fix linting --- docs/pages/benchmarking.md | 14 +++++++------- docs/pages/bindings.md | 12 ++++++------ docs/pages/ci.md | 18 +++++++++--------- docs/pages/dev.md | 32 ++++++++++++++++---------------- docs/pages/docs.md | 4 ++-- docs/pages/linting.md | 32 ++++++++++++++++---------------- docs/pages/packaging.md | 18 +++++++++--------- docs/pages/templates.md | 12 ++++++------ docs/pages/testing.md | 12 ++++++------ 9 files changed, 77 insertions(+), 77 deletions(-) diff --git a/docs/pages/benchmarking.md b/docs/pages/benchmarking.md index 41d08848..3f0a8f0e 100644 --- a/docs/pages/benchmarking.md +++ b/docs/pages/benchmarking.md @@ -6,10 +6,10 @@ layout: default # Benchmarking | Name | Short description | 🚦 | Used by | -| ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------| :-: | -| [pyinstrument](https://pyinstrument.readthedocs.io/en/stable) | Python profiler. Tells you how long individual lines of code take to run, so you can focus on the slowest part of your program to speed it up. | 🟒 | | -| [snakeviz](https://jiffyclub.github.io/snakeviz/) | Browser based graphical viewer for the output of Python’s cProfile module. | 🟒 | | -| [asv](https://asv.readthedocs.io/en/stable/) | A tool for benchmarking Python packages over their lifetime. Allows you to write benchmarks and then run them against every commit in the repository, to identify where performance increased or decreased. | 🟒 | | -| [memray](https://bloomberg.github.io/memray/) | Memray tracks and reports memory allocations, both in Python code and in compiled extension modules. It also has a [plugin](https://pytest-memray.readthedocs.io/en/latest/) for easy integration with pytest. However, it only works on Linux and MacOS, and cannot be installed on other platforms. | 🟠 | | -| [line_profiler](https://pypi.org/project/line-profiler/) | It is a module for doing line-by-line profiling of functions. | 🟠 | | -| [memory_profiler](https://pypi.org/project/memory-profiler/) | This package is no longer actively maintained. It is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption. | πŸ”΄ | | +| ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | :-----: | +| [pyinstrument](https://pyinstrument.readthedocs.io/en/stable) | Python profiler. Tells you how long individual lines of code take to run, so you can focus on the slowest part of your program to speed it up. | 🟒 | | +| [snakeviz](https://jiffyclub.github.io/snakeviz/) | Browser based graphical viewer for the output of Python’s cProfile module. | 🟒 | | +| [asv](https://asv.readthedocs.io/en/stable/) | A tool for benchmarking Python packages over their lifetime. Allows you to write benchmarks and then run them against every commit in the repository, to identify where performance increased or decreased. | 🟒 | | +| [memray](https://bloomberg.github.io/memray/) | Memray tracks and reports memory allocations, both in Python code and in compiled extension modules. It also has a [plugin](https://pytest-memray.readthedocs.io/en/latest/) for easy integration with pytest. However, it only works on Linux and MacOS, and cannot be installed on other platforms. | 🟠 | | +| [line_profiler](https://pypi.org/project/line-profiler/) | It is a module for doing line-by-line profiling of functions. | 🟠 | | +| [memory_profiler](https://pypi.org/project/memory-profiler/) | This package is no longer actively maintained. It is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption. | πŸ”΄ | | diff --git a/docs/pages/bindings.md b/docs/pages/bindings.md index d16ad205..db1f2002 100644 --- a/docs/pages/bindings.md +++ b/docs/pages/bindings.md @@ -6,9 +6,9 @@ layout: default # Bindings | Name | Short description | 🚦 | Used by | -| --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | ----| :-: | -| [Cython](https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html) | C/C++ binding library with numpy array integration | 🟒 | | -| [ctypes](https://docs.python.org/3.8/library/ctypes.html) | Native python method for calling functions in shared C libraries | 🟠 | | -| [pybind11](https://github.com/pybind/pybind11) | Bindings to C++ with a steep learning curve | 🟠 | | -| [f2py](https://numpy.org/devdocs/f2py/f2py.getting-started.html) | Bindings to Fortran developed by numpy | 🟠 | | -| [pyO3](https://github.com/PyO3/pyo3) | Straightforward bindings to rust with support for [packaging](https://github.com/PyO3/maturin) | 🟒 | | +| --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------- | --- | :-----: | +| [Cython](https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html) | C/C++ binding library with numpy array integration | 🟒 | | +| [ctypes](https://docs.python.org/3.8/library/ctypes.html) | Native python method for calling functions in shared C libraries | 🟠 | | +| [pybind11](https://github.com/pybind/pybind11) | Bindings to C++ with a steep learning curve | 🟠 | | +| [f2py](https://numpy.org/devdocs/f2py/f2py.getting-started.html) | Bindings to Fortran developed by numpy | 🟠 | | +| [pyO3](https://github.com/PyO3/pyo3) | Straightforward bindings to rust with support for [packaging](https://github.com/PyO3/maturin) | 🟒 | | diff --git a/docs/pages/ci.md b/docs/pages/ci.md index 39eaf286..bae2d5c4 100644 --- a/docs/pages/ci.md +++ b/docs/pages/ci.md @@ -5,12 +5,12 @@ layout: default # Continuous integration -| Name | Short description | 🚦 | Used by | -| ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-: | -| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED](https://github.com/UCL-ARC/rred-reports) | -| [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | -| [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | -| [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | | +| Name | Short description | 🚦 | Used by | +| ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED](https://github.com/UCL-ARC/rred-reports) | +| [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | +| [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | +| [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | |
🟒 explanation @@ -20,6 +20,6 @@ We have many projects using github CI, it's both convenient and works well. It's # Coverage monitoring | Name | Short description | 🚦 | Used by | -| ---------------------------------------- | ----------------------------------------------- | ---- | :-: | -| [Codecov](https://docs.codecov.com/docs) | Hosted service to report code coverage metrics. | 🟒 | | -| [Coveralls](https://docs.coveralls.io/) | Hosted service to report code coverage metrics. | 🟠 | | +| ---------------------------------------- | ----------------------------------------------- | --- | :-----: | +| [Codecov](https://docs.codecov.com/docs) | Hosted service to report code coverage metrics. | 🟒 | | +| [Coveralls](https://docs.coveralls.io/) | Hosted service to report code coverage metrics. | 🟠 | | diff --git a/docs/pages/dev.md b/docs/pages/dev.md index 8b0dfd4b..ac1f28d7 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -6,26 +6,26 @@ layout: default # Integrated Development Environments (IDEs) | Name | Short description | 🚦 | Used by | -| -------------------------------------------------------- | ----------------------------------- | ---- | :-: | -| [Visual Studio Code](https://code.visualstudio.com/docs) | A light-weight general-purpose IDE. | 🟠 | | -| [PyCharm](https://www.jetbrains.com/pycharm/) | A Python IDE by JetBrains. | 🟠 | | +| -------------------------------------------------------- | ----------------------------------- | --- | :-----: | +| [Visual Studio Code](https://code.visualstudio.com/docs) | A light-weight general-purpose IDE. | 🟠 | | +| [PyCharm](https://www.jetbrains.com/pycharm/) | A Python IDE by JetBrains. | 🟠 | | # Virtual environments | Name | Short description | 🚦 | Used by | -| --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | ---- | :-: | -| [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) | A tool to manage conda environments. Faster than conda for installing dependencies. | 🟒 | | -| [conda](https://conda.io/projects/conda/en/latest/) | Conda quickly installs, runs, and updates packages and their dependencies. | 🟠 | | -| [pipenv](https://pipenv.pypa.io/en/latest/) | A tool that automatically creates and manages a virtualenv for your projects. | 🟠 | | -| [venv](https://docs.python.org/3/library/venv.html) | A tool to create isolated Python environments. | πŸ”΄ | | -| [virtualenv](https://virtualenv.pypa.io/en/latest/) | A tool to create isolated Python environments which offers more features than venv. | 🟠 | | -| [pyenv](https://github.com/pyenv/pyenv) | A tool that lets you easily switch between multiple versions of Python. | 🟠 | | +| --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | --- | :-----: | +| [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) | A tool to manage conda environments. Faster than conda for installing dependencies. | 🟒 | | +| [conda](https://conda.io/projects/conda/en/latest/) | Conda quickly installs, runs, and updates packages and their dependencies. | 🟠 | | +| [pipenv](https://pipenv.pypa.io/en/latest/) | A tool that automatically creates and manages a virtualenv for your projects. | 🟠 | | +| [venv](https://docs.python.org/3/library/venv.html) | A tool to create isolated Python environments. | πŸ”΄ | | +| [virtualenv](https://virtualenv.pypa.io/en/latest/) | A tool to create isolated Python environments which offers more features than venv. | 🟠 | | +| [pyenv](https://github.com/pyenv/pyenv) | A tool that lets you easily switch between multiple versions of Python. | 🟠 | | # Other -| Name | Short description | 🚦 | Used by | -| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-: | -| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | -| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer,](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) [Puppet Submitty,](https://github.com/UCL-ARC/puppet-submitty) [Quality Workflow tool](https://github.com/UCL-ARC/qw) | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | +| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | +| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | +| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer,](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) [Puppet Submitty,](https://github.com/UCL-ARC/puppet-submitty) [Quality Workflow tool](https://github.com/UCL-ARC/qw) | diff --git a/docs/pages/docs.md b/docs/pages/docs.md index c668c73d..252cb2d9 100644 --- a/docs/pages/docs.md +++ b/docs/pages/docs.md @@ -8,9 +8,9 @@ layout: default ## Doc building | Name | Short description | 🚦 | Used by | -| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ---------------------------------------------------------------------- | +| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ---------------------------------------------------------------------- | --- | | [sphinx](https://www.sphinx-doc.org/en/master/) | Generates documentation from reStructuredText or Markdown files | 🟒 | [WAZP](https://github.com/SainsburyWellcomeCentre/WAZP/tree/main/docs) | -| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | +| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | | [pdoc](https://pdoc.dev/) | Auto-generates API documentation from docstrings | 🟠 | [MICI](https://github.com/matt-graham/mici) | | [gitbook](https://www.gitbook.com/) | General documentation builder; integrates with GitHub | 🟠 | | diff --git a/docs/pages/linting.md b/docs/pages/linting.md index 2dea3528..697701c2 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -9,20 +9,20 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b ## Code formatting -| Name | Short description | 🚦 | Used by | -| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---- | :-: | +| Name | Short description | 🚦 | Used by | +| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | -| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi)| -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi)| -| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | -| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | -| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | -| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | | -| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | | -| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | | -| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | | -| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | | +| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | +| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | +| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | +| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | | +| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | | +| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | | +| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | | +| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | |
🟒 explanation @@ -44,6 +44,6 @@ Flake8 is not recommended because it doesn't support `pyproject.toml` and [seemi ## Type checking -| Name | Short description | 🚦 | Used by | -| ---------------------------------------------- | ----------------------------------------------------------------------------- | ----- | :-: | -| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------------- | ----------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | diff --git a/docs/pages/packaging.md b/docs/pages/packaging.md index 479f7b7f..a97de7d6 100644 --- a/docs/pages/packaging.md +++ b/docs/pages/packaging.md @@ -5,17 +5,17 @@ layout: default # Packaging -| Name | Short description | 🚦 | Used by | -| --------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------- | :-: | -| [build](https://pypa-build.readthedocs.io/en/stable/) | Straightforward tool to build a Python package. | 🟒 | | -| [setuptools](https://setuptools.pypa.io) | A widely used build backend, used to configure a Python package. | 🟒 | [autodE](https://github.com/duartegroup/autodE) | -| [setuptools-scm](https://github.com/pypa/setuptools_scm/) | Provides automatic versioning Python packages. Also automatically adds all files under source control to the sdist / wheel. | 🟒 | [btrack](https://github.com/quantumjot/btrack) | -| [cibuildwheel](https://cibuildwheel.readthedocs.io) | Builds python wheels for the main operating systems on continuous integration runs (e.g. GitHub actions). | 🟒 | [streamtracer](https://github.com/dstansby/streamtracer) | +| Name | Short description | 🚦 | Used by | +| --------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------- | --- | :------------------------------------------------------: | +| [build](https://pypa-build.readthedocs.io/en/stable/) | Straightforward tool to build a Python package. | 🟒 | | +| [setuptools](https://setuptools.pypa.io) | A widely used build backend, used to configure a Python package. | 🟒 | [autodE](https://github.com/duartegroup/autodE) | +| [setuptools-scm](https://github.com/pypa/setuptools_scm/) | Provides automatic versioning Python packages. Also automatically adds all files under source control to the sdist / wheel. | 🟒 | [btrack](https://github.com/quantumjot/btrack) | +| [cibuildwheel](https://cibuildwheel.readthedocs.io) | Builds python wheels for the main operating systems on continuous integration runs (e.g. GitHub actions). | 🟒 | [streamtracer](https://github.com/dstansby/streamtracer) | ## Conda These tools are helpful if you're looking to publish your package on [conda-forge](https://conda-forge.org/), so users can install it through the [conda](https://docs.conda.io/en/latest/) or [mamba](https://mamba.readthedocs.io/en/latest/index.html) package managers. -| Name | Short description | 🚦 | Used by | -| --------------------------------------------------------- | --------------------------------------------------------------------------- | ------- | :-: | -| [GraySkull](https://github.com/conda-incubator/grayskull) | A tool for automatic conda recipe generation (aimed at conda-forge, above). | 🟒 | | +| Name | Short description | 🚦 | Used by | +| --------------------------------------------------------- | --------------------------------------------------------------------------- | --- | :-----: | +| [GraySkull](https://github.com/conda-incubator/grayskull) | A tool for automatic conda recipe generation (aimed at conda-forge, above). | 🟒 | | diff --git a/docs/pages/templates.md b/docs/pages/templates.md index 2cb5a060..912ed330 100644 --- a/docs/pages/templates.md +++ b/docs/pages/templates.md @@ -30,9 +30,9 @@ If you're making a package within one of these communities, we recommend using t These are packages that can be used for creating your own package template. | Name | Short description | 🚦 | Used by | -| ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | ----- | :-: | -| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates, but is not maintained. | πŸ”΄ | | -| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is actively maintained. | 🟒 | | -| [Cruft](https://github.com/cruft/cruft) | Can be used to create projects from a cookiecutter template and to keep the project configuration in sync with the template. | 🟠 | | -| [Copier](https://github.com/copier-org/copier) | A tool to create project templates that are highly configurable. Project configuration can be kept in sync with the templae. | 🟠 | | -| [GitHub templates](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) | GitHub repositories can be used as templates, but they are not configurable. | 🟠 | | +| ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | --- | :-----: | +| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates, but is not maintained. | πŸ”΄ | | +| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is actively maintained. | 🟒 | | +| [Cruft](https://github.com/cruft/cruft) | Can be used to create projects from a cookiecutter template and to keep the project configuration in sync with the template. | 🟠 | | +| [Copier](https://github.com/copier-org/copier) | A tool to create project templates that are highly configurable. Project configuration can be kept in sync with the templae. | 🟠 | | +| [GitHub templates](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) | GitHub repositories can be used as templates, but they are not configurable. | 🟠 | | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 635183ef..7b804981 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -7,11 +7,11 @@ layout: default ## Test runners -| Name | Short description | 🚦 | Used by | -| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | ---- | :-: | -| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | | [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | -| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | | +| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
🟒 explanation @@ -20,7 +20,7 @@ We recommend `pytest` over `unittest` because `pytest` tends to encourage a clea ## pytest plugins -| Name | Short description | 🚦 | Used by | -| ---------------------------------------------------------------------- | ------------------------------------------------------------------------- | ---- | :-: | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------------------------------------- | ------------------------------------------------------------------------- | --- | :-------------------------------------------------: | | [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/index.html) | A framework to generate coverage reports that plays nicely with `pytest`. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | | [pytest-mock](https://pytest-mock.readthedocs.io/en/latest/index.html) | A framework to mock/patch objects that plays nicely with `pytest`. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | From 771aa9dffedd801017e2072f95e84be23f05e3c2 Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Tue, 24 Oct 2023 16:33:08 +0100 Subject: [PATCH 07/12] Move commas after link --- docs/pages/linting.md | 10 +++++----- docs/pages/testing.md | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/pages/linting.md b/docs/pages/linting.md index 697701c2..eec1192a 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -11,10 +11,10 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b | Name | Short description | 🚦 | Used by | | -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | -| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED,](https://github.com/UCL-ARC/rred-reports) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [TREx,](https://github.com/UCL-ARC/TREx) [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi), [autodE](https://github.com/duartegroup/autodE) | +| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | | [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | | [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | | [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | @@ -46,4 +46,4 @@ Flake8 is not recommended because it doesn't support `pyproject.toml` and [seemi | Name | Short description | 🚦 | Used by | | ---------------------------------------------- | ----------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [HIP-CT-CZI,](https://github.com/UCL-ARC/hip-ct-czi) [autodE](https://github.com/duartegroup/autodE) | +| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi), [autodE](https://github.com/duartegroup/autodE) | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 7b804981..26ed08f2 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -9,8 +9,8 @@ layout: default | Name | Short description | 🚦 | Used by | | ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | -| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | +| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports), [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | +| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
From 7eeda5788dbfb93fbabe82d25a144f5e13902695 Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Tue, 24 Oct 2023 16:35:29 +0100 Subject: [PATCH 08/12] Move more commas --- docs/pages/ci.md | 2 +- docs/pages/dev.md | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/pages/ci.md b/docs/pages/ci.md index bae2d5c4..31b139b3 100644 --- a/docs/pages/ci.md +++ b/docs/pages/ci.md @@ -7,7 +7,7 @@ layout: default | Name | Short description | 🚦 | Used by | | ------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration,](https://github.com/SainsburyWellcomeCentre/crabs-exploration) [DiRAC,](https://github.com/UCL-ARC/dirac-swift-api) [RRED](https://github.com/UCL-ARC/rred-reports) | +| [GitHub Actions](https://docs.github.com/en/actions) | Continuous integration and continuous delivery platform (integrated with GitHub). | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports) | | [Travis CI](https://docs.travis-ci.com/) | Continuous integration and continuous delivery platform. | 🟠 | | | [AppVeyor](https://www.appveyor.com/docs/) | Continuous integration and continuous delivery platform. | 🟠 | | | [Bamboo](https://confluence.atlassian.com/bamboo/bamboo-documentation-289276551.html) | Atlassian continuous integration and continuous delivery platform. | 🟠 | | diff --git a/docs/pages/dev.md b/docs/pages/dev.md index ac1f28d7..739a9360 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -27,5 +27,5 @@ layout: default | ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | | [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | -| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED,](https://github.com/UCL-ARC/rred-reports) [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer,](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) [Puppet Submitty,](https://github.com/UCL-ARC/puppet-submitty) [Quality Workflow tool](https://github.com/UCL-ARC/qw) | +| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports), [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | +| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE), [Puppet Submitty](https://github.com/UCL-ARC/puppet-submitty), [Quality Workflow tool](https://github.com/UCL-ARC/qw) | From 8b4fcfaaeaa2ed846908dafc2d461be31aa77c13 Mon Sep 17 00:00:00 2001 From: nikk-nikaznan Date: Tue, 24 Oct 2023 17:14:54 +0100 Subject: [PATCH 09/12] removed private link --- docs/Gemfile.lock | 4 ++-- docs/pages/dev.md | 12 ++++++------ docs/pages/docs.md | 12 ++++++------ docs/pages/linting.md | 34 +++++++++++++++++----------------- docs/pages/testing.md | 10 +++++----- 5 files changed, 36 insertions(+), 36 deletions(-) diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index e1f4727e..cc9f652c 100644 --- a/docs/Gemfile.lock +++ b/docs/Gemfile.lock @@ -26,7 +26,7 @@ GEM liquid (~> 4.0) mercenary (>= 0.3.6, < 0.5) pathutil (~> 0.9) - rouge (>= 3.0, < 5.0) + rogue (>= 3.0, < 5.0) safe_yaml (~> 1.0) terminal-table (>= 1.8, < 4.0) webrick (~> 1.7) @@ -60,7 +60,7 @@ GEM rb-inotify (0.10.1) ffi (~> 1.0) rexml (3.2.6) - rouge (4.1.3) + rogue (4.1.3) safe_yaml (1.0.5) sassc (2.4.0) ffi (~> 1.9) diff --git a/docs/pages/dev.md b/docs/pages/dev.md index 739a9360..da702a89 100644 --- a/docs/pages/dev.md +++ b/docs/pages/dev.md @@ -23,9 +23,9 @@ layout: default # Other -| Name | Short description | 🚦 | Used by | -| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | -| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports), [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE) | -| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Conjurer](https://github.com/UCL-ARC/Conjurer/tree/main/MLDE), [Puppet Submitty](https://github.com/UCL-ARC/puppet-submitty), [Quality Workflow tool](https://github.com/UCL-ARC/qw) | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------- | ------------------------------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------: | +| [jedi](https://jedi.readthedocs.io/en/latest/) | Refactoring and autocompletion used in IDEs. | 🟒 | | +| [rope](https://rope.readthedocs.io/en/latest/overview.html) | Refactoring library. | | | +| [tqdm](https://pypi.org/project/tqdm/2.2.3/) | Progress bar for loops. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports) | +| [psutil](https://psutil.readthedocs.io/en/latest/) | System monitoring, profiling, limiting process resources and the management of running processes. | 🟒 | [Puppet Submitty](https://github.com/UCL-ARC/puppet-submitty), [Quality Workflow tool](https://github.com/UCL-ARC/qw) | diff --git a/docs/pages/docs.md b/docs/pages/docs.md index 252cb2d9..f922e049 100644 --- a/docs/pages/docs.md +++ b/docs/pages/docs.md @@ -7,12 +7,12 @@ layout: default ## Doc building -| Name | Short description | 🚦 | Used by | -| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ---------------------------------------------------------------------- | --- | -| [sphinx](https://www.sphinx-doc.org/en/master/) | Generates documentation from reStructuredText or Markdown files | 🟒 | [WAZP](https://github.com/SainsburyWellcomeCentre/WAZP/tree/main/docs) | -| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | | -| [pdoc](https://pdoc.dev/) | Auto-generates API documentation from docstrings | 🟠 | [MICI](https://github.com/matt-graham/mici) | -| [gitbook](https://www.gitbook.com/) | General documentation builder; integrates with GitHub | 🟠 | | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ----------------------------------------------------------------------------------------------------- | --- | +| [sphinx](https://www.sphinx-doc.org/en/master/) | Generates documentation from reStructuredText or Markdown files | 🟒 | [WAZP](https://github.com/SainsburyWellcomeCentre/WAZP/tree/main/docs) | +| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | | | +| [pdoc](https://pdoc.dev/) | Auto-generates API documentation from docstrings | 🟠 | [sleplet](https://github.com/astro-informatics/sleplet/), [MICI](https://github.com/matt-graham/mici) | +| [gitbook](https://www.gitbook.com/) | General documentation builder; integrates with GitHub | 🟠 | |
🟒 explanation diff --git a/docs/pages/linting.md b/docs/pages/linting.md index eec1192a..16edf426 100644 --- a/docs/pages/linting.md +++ b/docs/pages/linting.md @@ -9,20 +9,20 @@ See [here for example configuration](https://github.com/UCL-ARC/python-tooling/b ## Code formatting -| Name | Short description | 🚦 | Used by | -| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | :-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi), [autodE](https://github.com/duartegroup/autodE) | -| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [TREx](https://github.com/UCL-ARC/TREx), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi) | -| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | -| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | -| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | -| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | | -| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | | -| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | | -| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | | -| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | | +| Name | Short description | 🚦 | Used by | +| -------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| [black](https://black.readthedocs.io/en/stable/) | Opinionated formatter, defaults to 88 characters per line. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [autodE](https://github.com/duartegroup/autodE) | +| [isort](https://pycqa.github.io/isort/) | Sorts imports alphabetically, splits into first/third party, works on python & cython code. | 🟒 | | +| [pre-commit](https://pre-commit.com/) | Universal tool which performs a git hook on commit, allows you to run linters/formatters on any code. A tool to automatically run many of the tools listed below. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [ruff](https://github.com/astral-sh/ruff) | A very fast linter which incorporates a range of other linters. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [RRED](https://github.com/UCL-ARC/rred-reports), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [toml-sort](https://toml-sort.readthedocs.io/en/latest/) | Sorts TOML files which are now part of PEP 8. | 🟒 | | +| [autopep8](https://github.com/hhatto/autopep8) | Formatter which conforms to PEP 8. | 🟠 | | +| [pycodestyle](https://pycodestyle.pycqa.org/en/latest/) | Linter which checks for errors. | 🟠 | | +| [pyflakes](https://github.com/PyCQA/pyflakes) | Linter which checks for errors. | 🟠 | | +| [pylint](https://pylint.readthedocs.io/en/latest/) | Linter which checks for errors. | 🟠 | | +| [sourcery](https://sourcery.ai/) | An AI code reviewer which simplifies code, has a free version but can pay for fancier features. | 🟠 | | +| [yapf](https://github.com/google/yapf) | Google formatter. | 🟠 | | +| [flake8](https://flake8.pycqa.org/en/latest/) | Linter which complains if code doesn't follow a rule. Does not support modern `pyproject.toml` configuration. | πŸ”΄ | |
🟒 explanation @@ -44,6 +44,6 @@ Flake8 is not recommended because it doesn't support `pyproject.toml` and [seemi ## Type checking -| Name | Short description | 🚦 | Used by | -| ---------------------------------------------- | ----------------------------------------------------------------------------- | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [HIP-CT-CZI](https://github.com/UCL-ARC/hip-ct-czi), [autodE](https://github.com/duartegroup/autodE) | +| Name | Short description | 🚦 | Used by | +| ---------------------------------------------- | ----------------------------------------------------------------------------- | --- | :--------------------------------------------------------------------------------------------------------------------------------: | +| [mypy](https://mypy.readthedocs.io/en/stable/) | Static type checker, won't fail if no typing but will if typing is incorrect. | 🟒 | [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [autodE](https://github.com/duartegroup/autodE) | diff --git a/docs/pages/testing.md b/docs/pages/testing.md index 26ed08f2..d2d60a91 100644 --- a/docs/pages/testing.md +++ b/docs/pages/testing.md @@ -7,11 +7,11 @@ layout: default ## Test runners -| Name | Short description | 🚦 | Used by | -| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | --- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports), [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | -| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration), [XNAT SRR](https://github.com/UCL-MIRSG/UCLH-MPBE-SRR-XNAT) | -| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | | +| Name | Short description | 🚦 | Used by | +| ----------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | --- | :------------------------------------------------------------------------------------------------------------------------------------: | +| [pytest](https://docs.pytest.org/en/stable/contents.html) | A framework for writing and running tests. | 🟒 | [RRED](https://github.com/UCL-ARC/rred-reports), [DiRAC](https://github.com/UCL-ARC/dirac-swift-api) | +| [tox](https://tox.wiki/en/latest/index.html) | A framework that allows running tests and packaging in different environments. | 🟒 | [DiRAC](https://github.com/UCL-ARC/dirac-swift-api), [Crabs Exploration](https://github.com/SainsburyWellcomeCentre/crabs-exploration) | +| [unittest](https://docs.python.org/dev/library/unittest.html#module-unittest) | A framework built in to Python for writing and running tests. | 🟠 | |
🟒 explanation From 0c0a244d0e69b435f15b05ce20934b7cdd16a856 Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Wed, 25 Oct 2023 12:23:04 +0100 Subject: [PATCH 10/12] Swap `cookiecutter` and `cookieninja` --- docs/pages/templates.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/pages/templates.md b/docs/pages/templates.md index 912ed330..5002c044 100644 --- a/docs/pages/templates.md +++ b/docs/pages/templates.md @@ -31,8 +31,8 @@ These are packages that can be used for creating your own package template. | Name | Short description | 🚦 | Used by | | ----------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | --- | :-----: | -| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates, but is not maintained. | πŸ”΄ | | -| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is actively maintained. | 🟒 | | +| [Cookiecutter](https://github.com/cookiecutter/cookiecutter) | Widely-used tool for creating project templates | 🟒 | | | [Cruft](https://github.com/cruft/cruft) | Can be used to create projects from a cookiecutter template and to keep the project configuration in sync with the template. | 🟠 | | | [Copier](https://github.com/copier-org/copier) | A tool to create project templates that are highly configurable. Project configuration can be kept in sync with the templae. | 🟠 | | | [GitHub templates](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-template-repository) | GitHub repositories can be used as templates, but they are not configurable. | 🟠 | | +| [Cookieninja](https://github.com/cookieninja-generator/cookieninja) | A fork of Cookiecutter that is not actively maintained. | πŸ”΄ | | From 1afd0b7f69f526f1604ddc81b50bfd0e442c5819 Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Wed, 25 Oct 2023 12:23:49 +0100 Subject: [PATCH 11/12] Fix table --- docs/pages/docs.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/pages/docs.md b/docs/pages/docs.md index f922e049..cf04bb57 100644 --- a/docs/pages/docs.md +++ b/docs/pages/docs.md @@ -8,9 +8,9 @@ layout: default ## Doc building | Name | Short description | 🚦 | Used by | -| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ----------------------------------------------------------------------------------------------------- | --- | +| ----------------------------------------------- | --------------------------------------------------------------- | :-: | ----------------------------------------------------------------------------------------------------- | | [sphinx](https://www.sphinx-doc.org/en/master/) | Generates documentation from reStructuredText or Markdown files | 🟒 | [WAZP](https://github.com/SainsburyWellcomeCentre/WAZP/tree/main/docs) | -| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | | | +| [mkdocs](https://www.mkdocs.org/) | Generates documentation from Markdown files | 🟠 | | | [pdoc](https://pdoc.dev/) | Auto-generates API documentation from docstrings | 🟠 | [sleplet](https://github.com/astro-informatics/sleplet/), [MICI](https://github.com/matt-graham/mici) | | [gitbook](https://www.gitbook.com/) | General documentation builder; integrates with GitHub | 🟠 | | From fa233738cdec845bb1fc0854c15ec178151b0c57 Mon Sep 17 00:00:00 2001 From: Paddy Roddy Date: Wed, 25 Oct 2023 14:18:09 +0100 Subject: [PATCH 12/12] Change back to `rouge` --- docs/Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index cc9f652c..e1f4727e 100644 --- a/docs/Gemfile.lock +++ b/docs/Gemfile.lock @@ -26,7 +26,7 @@ GEM liquid (~> 4.0) mercenary (>= 0.3.6, < 0.5) pathutil (~> 0.9) - rogue (>= 3.0, < 5.0) + rouge (>= 3.0, < 5.0) safe_yaml (~> 1.0) terminal-table (>= 1.8, < 4.0) webrick (~> 1.7) @@ -60,7 +60,7 @@ GEM rb-inotify (0.10.1) ffi (~> 1.0) rexml (3.2.6) - rogue (4.1.3) + rouge (4.1.3) safe_yaml (1.0.5) sassc (2.4.0) ffi (~> 1.9)