From 6047e9a673b0a93b870f20a0c173620c6f022b6f Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 11:19:54 +0200 Subject: [PATCH 1/6] rst for pypi, zip file install --- requirements-dev.txt | 5 ++++- setup.py | 11 +++-------- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index cffade5..aefbeff 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,3 +1,6 @@ # syntax check, unit test, profiling flake8>=3.8.4 -pytest>=6.1.2 +pytest>=6.2.1 +twine==3.3.0 +pypandoc>=1.5 +wheel>=0.31.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 31fa742..5873dc5 100644 --- a/setup.py +++ b/setup.py @@ -1,16 +1,11 @@ from setuptools import setup - - -def read(fname): - import os - return open(os.path.join(os.path.dirname(__file__), fname)).read() +import pypandoc setup(name='scipy-tweaks', version='0.1.1', description='Utility functions for scipy.', - long_description=read('README.md'), - long_description_content_type='text/markdown', + long_description=pypandoc.convert('README.md', 'rst'), url='http://github.com/ulf1/scipy-tweaks', author='Ulf Hamster', author_email='554c46@gmail.com', @@ -20,4 +15,4 @@ def read(fname): 'setuptools>=40.0.0', 'scipy>=1.5.4'], python_requires='>=3.6', - zip_safe=False) + zip_safe=True) From be219311e4077acaf71761623e809aa1dcdc956e Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 12:34:30 +0200 Subject: [PATCH 2/6] pkg version variable added --- scipy_tweaks/__init__.py | 2 ++ setup.py | 12 +++++++++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/scipy_tweaks/__init__.py b/scipy_tweaks/__init__.py index e92fb85..23a319e 100644 --- a/scipy_tweaks/__init__.py +++ b/scipy_tweaks/__init__.py @@ -1 +1,3 @@ +__version__ = '0.1.2' + from .idseqs_to_mask import idseqs_to_mask diff --git a/setup.py b/setup.py index 5873dc5..d368557 100644 --- a/setup.py +++ b/setup.py @@ -2,8 +2,18 @@ import pypandoc +def get_version(path): + with open(path, "r") as fp: + lines = fp.read() + for line in lines.split("\n"): + if line.startswith('__version__'): + delim = '"' if '"' in line else "'" + return line.split(delim)[1] + raise RuntimeError("Unable to find version string.") + + setup(name='scipy-tweaks', - version='0.1.1', + version=get_version("scipy_tweaks/__init__.py"), description='Utility functions for scipy.', long_description=pypandoc.convert('README.md', 'rst'), url='http://github.com/ulf1/scipy-tweaks', From ad86313b57d5d5c791a07ab4406353598b09a380 Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 15:16:24 +0200 Subject: [PATCH 3/6] funding added --- .github/FUNDING.yml | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 .github/FUNDING.yml diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 0000000..42a4ce9 --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1,3 @@ +github: [ulf1] +patreon: ulfhamster +ko_fi: ulfhamster From 704e9df15391821e607dffd60adf251c6db59a44 Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 17:41:45 +0200 Subject: [PATCH 4/6] license changed to apcahe 2 --- LICENSE | 222 ++++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 201 insertions(+), 21 deletions(-) diff --git a/LICENSE b/LICENSE index ebaea70..672cb27 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,201 @@ -MIT License - -Copyright (c) 2020 Ulf Hamster - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2021 Ulf Hamster + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file From 547e0f8549b52fd24807f1ca88429b5d7d990ac7 Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 17:42:10 +0200 Subject: [PATCH 5/6] cosmetic docs stuff, requirements corrected --- README.md | 30 +++++++++++------------------- requirements-demo.txt | 2 +- requirements.txt | 2 +- setup.py | 2 +- 4 files changed, 14 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 6ce7120..2371bb3 100644 --- a/README.md +++ b/README.md @@ -2,15 +2,14 @@ Utility functions for scipy. -## Table of Contents -* [Installation](#installation) -* [Usage](#usage) -* [Commands](#commands) -* [Support](#support) -* [Contributing](#contributing) +## Usage +Check the [examples](http://github.com/ulf1/scipy-tweaks/examples) folder for notebooks. + +## Appendix -## Installation + +### Installation The `scipy-tweaks` [git repo](http://github.com/ulf1/scipy-tweaks) is available as [PyPi package](https://pypi.org/project/scipy-tweaks) ``` @@ -18,13 +17,7 @@ pip install scipy-tweaks pip install git+ssh://git@github.com/ulf1/scipy-tweaks.git ``` - -## Usage -Check the [examples](http://github.com/ulf1/scipy-tweaks/examples) folder for notebooks. - - -## Commands -Install a virtual environment +### Install a virtual environment ``` python3.6 -m venv .venv @@ -37,14 +30,14 @@ pip3 install -r requirements-demo.txt (If your git repo is stored in a folder with whitespaces, then don't use the subfolder `.venv`. Use an absolute path without whitespaces.) -Python commands +### Python commands * Jupyter for the examples: `jupyter lab` * Check syntax: `flake8 --ignore=F401 --exclude=$(grep -v '^#' .gitignore | xargs | sed -e 's/ /,/g')` * Run Unit Tests: `pytest` * Upload to PyPi with twine: `python setup.py sdist && twine upload -r pypi dist/*` -Clean up +### Clean up ``` find . -type f -name "*.pyc" | xargs rm @@ -53,10 +46,9 @@ rm -r .pytest_cache rm -r .venv ``` - -## Support +### Support Please [open an issue](https://github.com/ulf1/scipy-tweaks/issues/new) for support. -## Contributing +### Contributing Please contribute using [Github Flow](https://guides.github.com/introduction/flow/). Create a branch, add commits, and [open a pull request](https://github.com/ulf1/scipy-tweaks/compare/). diff --git a/requirements-demo.txt b/requirements-demo.txt index 37ea3fd..bbaf02a 100644 --- a/requirements-demo.txt +++ b/requirements-demo.txt @@ -1,3 +1,3 @@ # packages required to run example notebooks -jupyterlab>=2.2.9 +jupyterlab>=3.0.0 # matplotlib>=3.3.2 diff --git a/requirements.txt b/requirements.txt index 678b92d..495ccdf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,2 +1,2 @@ # public packages (see setup.py) -scipy>=1.5.4 +scipy>=1.5.4,<2 diff --git a/setup.py b/setup.py index d368557..c0996cb 100644 --- a/setup.py +++ b/setup.py @@ -23,6 +23,6 @@ def get_version(path): packages=['scipy_tweaks'], install_requires=[ 'setuptools>=40.0.0', - 'scipy>=1.5.4'], + 'scipy>=1.5.4,<2'], python_requires='>=3.6', zip_safe=True) From 5a5246234092c721559b903a5b0f7d6ad6b32651 Mon Sep 17 00:00:00 2001 From: UH <554c46@gmail.com> Date: Thu, 8 Apr 2021 17:45:00 +0200 Subject: [PATCH 6/6] change notice --- CHANGES.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGES.md b/CHANGES.md index 737f361..300d3c0 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,7 @@ +# 0.1.2 / 2021-04-08 + + * MIT License replaced by Apache 2.0 + # 0.1.1 / 2020-11-06 * required python version downgraded from 3.8 to 3.6