From 51d203abe1ff33538cf6e3444ca7f0ac60d8a407 Mon Sep 17 00:00:00 2001 From: Tom Donoghue Date: Wed, 17 Sep 2025 15:56:24 +0100 Subject: [PATCH 1/4] update install instructions --- README.rst | 34 ++++++++++++++++++++++++++-------- 1 file changed, 26 insertions(+), 8 deletions(-) diff --git a/README.rst b/README.rst index c401ec4..ab976b3 100644 --- a/README.rst +++ b/README.rst @@ -93,24 +93,42 @@ There are also optional dependencies, that offer extra functionality: Installation ------------ -The current release version is the 0.4.X series. +The current release version of `hsntools` is the 1.X.X release series. -Check the +See the `changelog `_ -for notes on updates and changes across versions. +for notes on major version releases. -This module should be installed from Github: +**Stable Release Version** -**Install from a clone** +To install the latest stable release, you can use pip: -First clone this repository, then move into the cloned repository, and install: +.. code-block:: shell + + $ pip install hsntools + +**Development Version** + +To get the current development version, first clone this repository: + +.. code-block:: shell + + $ git clone https://github.com/hsnpipeline/hsntools + +To install this cloned copy, move into the directory you just cloned, and run: .. code-block:: shell - $ git clone https://github.com/HSNPipeline/hsntools - $ cd hsntools $ pip install . +**Editable Version** + +To install an editable version, download the development version as above, and run: + +.. code-block:: shell + + $ pip install -e . + Contribute ---------- From c676bd1907a7e563ff8c5248fc1905842ece323e Mon Sep 17 00:00:00 2001 From: Tom Donoghue Date: Wed, 17 Sep 2025 16:04:35 +0100 Subject: [PATCH 2/4] update optional req mgmt --- optional-requirements.txt | 6 +++--- setup.py | 8 +++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/optional-requirements.txt b/optional-requirements.txt index c9411dd..df231cf 100644 --- a/optional-requirements.txt +++ b/optional-requirements.txt @@ -1,8 +1,8 @@ -pynwb matplotlib +scipy scikit-learn pandas -scipy h5py +pynwb +neo mat73 -neo \ No newline at end of file diff --git a/setup.py b/setup.py index 8abd772..32423b6 100644 --- a/setup.py +++ b/setup.py @@ -53,9 +53,11 @@ install_requires = install_requires, tests_require = ['pytest'], extras_require = { - 'compute' : ['scipy', 'scikit-learn'], - 'data' : ['pandas', 'h5py', 'pynwb'], 'plot' : ['matplotlib'], - 'all' : ['scipy', 'scikit-learn', 'pandas', 'h5py', 'pynwb', 'matplotlib'], + 'timestamps' : ['scipy', 'scikit-learn'], + 'nwb' : ['h5py', 'pynwb'], + 'files' : ['scipy', 'pandas', 'h5py', 'pynwb', 'neo', 'mat73'], + 'all' : ['matplotlib', 'scipy', 'scikit-learn', 'pandas', 'h5py', 'pynwb', 'neo', 'mat73'], + 'tests' : ['pytest'], } ) \ No newline at end of file From 299a2c3cfb93bd77b963151a68b4bb209e61f99f Mon Sep 17 00:00:00 2001 From: Tom Donoghue Date: Wed, 17 Sep 2025 16:06:30 +0100 Subject: [PATCH 3/4] twaek metadata --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 32423b6..c495ee4 100644 --- a/setup.py +++ b/setup.py @@ -18,14 +18,14 @@ setup( name = 'hsntools', version = __version__, - description = 'Code for working with the Human Single-Neuron Pipeline', + description = 'Code for working with the Human Single-Neuron Pipeline.', long_description = long_description, long_description_content_type = 'text/x-rst', python_requires = '>=3.7', packages = find_packages(), license = 'MIT License', classifiers = [ - 'Development Status :: 4 - Beta', + 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering', 'License :: OSI Approved :: MIT License', @@ -57,7 +57,7 @@ 'timestamps' : ['scipy', 'scikit-learn'], 'nwb' : ['h5py', 'pynwb'], 'files' : ['scipy', 'pandas', 'h5py', 'pynwb', 'neo', 'mat73'], - 'all' : ['matplotlib', 'scipy', 'scikit-learn', 'pandas', 'h5py', 'pynwb', 'neo', 'mat73'], 'tests' : ['pytest'], + 'all' : ['matplotlib', 'scipy', 'scikit-learn', 'pandas', 'h5py', 'pynwb', 'neo', 'mat73', 'pytest'], } ) \ No newline at end of file From 5b7fbf3f7d4f22fd89783531b7e928763936638b Mon Sep 17 00:00:00 2001 From: Tom Donoghue Date: Wed, 17 Sep 2025 16:12:11 +0100 Subject: [PATCH 4/4] add readme badges --- README.rst | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index ab976b3..b072c17 100644 --- a/README.rst +++ b/README.rst @@ -1,12 +1,16 @@ hsntools ======== -|ProjectStatus| |BuildStatus| |Coverage| +|ProjectStatus| |Version| |BuildStatus| |Coverage| |License| |PythonVersions| .. |ProjectStatus| image:: http://www.repostatus.org/badges/latest/active.svg :target: https://www.repostatus.org/#active :alt: project status +.. |Version| image:: https://img.shields.io/pypi/v/hsntools.svg + :target: https://pypi.org/project/hsntools/ + :alt: version + .. |BuildStatus| image:: https://github.com/HSNPipeline/hsntools/actions/workflows/build.yml/badge.svg :target: https://github.com/HSNPipeline/hsntools/actions/workflows/build.yml :alt: build statue @@ -15,6 +19,14 @@ hsntools :target: https://codecov.io/gh/HSNPipeline/hsntools :alt: coverage +.. |License| image:: https://img.shields.io/pypi/l/hsntools.svg + :target: https://opensource.org/license/mit + :alt: license + +.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/hsntools.svg + :target: https://pypi.org/project/hsntools/ + :alt: python versions + ``hsntools`` (formerly 'convnwb') is a module for working with the Human Single-Neuron Pipeline (HSNPipeline). Overview