From 1aeb4508fabefa26cdbe38f53c2485feb5a6e54c Mon Sep 17 00:00:00 2001 From: samoturk Date: Mon, 25 Aug 2014 11:25:54 +0200 Subject: [PATCH 1/6] Added: orange, RDKit, Open Babel, cclib and Biopython --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index b3f54a9..e3c22b7 100644 --- a/README.md +++ b/README.md @@ -839,6 +839,12 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [SymPy](https://github.com/sympy/sympy) - A Python library for symbolic mathematics. * [statsmodels](https://github.com/statsmodels/statsmodels) - Statistical modeling and econometrics in Python. * [astropy](http://www.astropy.org/) - A community Python library for Astronomy. +* [orange](http://orange.biolab.si/) - Data mining, data visualization, analysis and machine learning through visual programming or Python scripting. +* [RDKit](http://www.rdkit.org/) - Cheminformatics and Machine Learning Software. +* [Open Babel](http://openbabel.org/wiki/Main_Page) - A chemical toolbox designed to speak the many languages of chemical data. +* [cclib](http://cclib.github.io/) - A library for parsing and interpreting the results of computational chemistry packages. +* [Biopython](http://biopython.org/wiki/Main_Page) - Biopython is a set of freely available tools for biological computation. + ## Data Visualization From 8e485323743dc35c95b480debcca30e0148b51e0 Mon Sep 17 00:00:00 2001 From: probar Date: Mon, 25 Aug 2014 16:58:46 +0200 Subject: [PATCH 2/6] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index b3f54a9..f0e14e2 100644 --- a/README.md +++ b/README.md @@ -126,6 +126,7 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [py2app](http://pythonhosted.org/py2app/) - Freezes Python scripts (Mac OS X). * [PyInstaller](http://www.pyinstaller.org/) - Converts Python programs into stand-alone executables (cross-platform). * [dh-virtualenv](http://dh-virtualenv.readthedocs.org/) - Build and distribute a virtualenv as a Debian package. +* [pynsist](http://pynsist.readthedocs.org/en/latest/) - build a full Windows installers.Installer will work even for people without python. ## Build Tools From c6b1e27db5a595c98003fba153533f7406df7892 Mon Sep 17 00:00:00 2001 From: probar Date: Thu, 28 Aug 2014 20:27:36 +0200 Subject: [PATCH 3/6] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index c38b9d6..1a318b1 100644 --- a/README.md +++ b/README.md @@ -725,6 +725,7 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [cryptography](https://cryptography.io/) - A package designed to expose cryptographic primitives and recipes to Python developers. * [PyNacl](https://github.com/pyca/pynacl) - Python binding to the Networking and Cryptography (NaCl) library. * [hashids](https://github.com/davidaurelio/hashids-python) - Implementation of [hashids](http://hashids.org) in Python. +* [Passlib](https://pythonhosted.org/passlib/index.html) - Secure password storage/hashing library, very high level ## GUI From 4b139beb118c231fb07a387df08d9dc04d84f62f Mon Sep 17 00:00:00 2001 From: Xuefeng Zhu Date: Thu, 28 Aug 2014 14:31:17 -0500 Subject: [PATCH 4/6] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index c38b9d6..c80b09f 100644 --- a/README.md +++ b/README.md @@ -991,6 +991,7 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [pluginbase](https://github.com/mitsuhiko/pluginbase) - A simple but flexible plugin system for Python. * [itsdangerous](https://github.com/mitsuhiko/itsdangerous) - Various helpers to pass trusted data to untrusted environments. * [blinker](https://github.com/jek/blinker) - A fast Python in-process signal/event dispatching system. +* [unp](https://github.com/mitsuhiko/unp) - Unpacks things ## Algorithms and Design Patterns From 2d49336fd2469e11894f494ed03f679ab7694ae6 Mon Sep 17 00:00:00 2001 From: samoturk Date: Fri, 29 Aug 2014 11:52:12 +0200 Subject: [PATCH 5/6] Added bcbb and bcbio-nextgen to Science and Data Analysis --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index e3c22b7..1194310 100644 --- a/README.md +++ b/README.md @@ -844,6 +844,9 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [Open Babel](http://openbabel.org/wiki/Main_Page) - A chemical toolbox designed to speak the many languages of chemical data. * [cclib](http://cclib.github.io/) - A library for parsing and interpreting the results of computational chemistry packages. * [Biopython](http://biopython.org/wiki/Main_Page) - Biopython is a set of freely available tools for biological computation. +* [bccb](https://github.com/chapmanb/bcbb) - Collection of useful code related to biological analysis. +* [bcbio-nextgen](https://github.com/chapmanb/bcbio-nextgen) - A toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. + ## Data Visualization From f8ea6a142bff5c35e9b7d8790b4b11c450453d80 Mon Sep 17 00:00:00 2001 From: Vinta Date: Mon, 1 Sep 2014 18:01:07 +0800 Subject: [PATCH 6/6] rearrange --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 5d7ab5d..13304de 100644 --- a/README.md +++ b/README.md @@ -94,10 +94,10 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [pyenv](https://github.com/yyuu/pyenv) - Simple Python version management. * [virtualenv](https://pypi.python.org/pypi/virtualenv) - A tool to create isolated Python environments. * [virtualenvwrapper](https://pypi.python.org/pypi/virtualenvwrapper) - A set of extensions to virtualenv +* [virtualenv-api](https://github.com/sjkingo/virtualenv-api) - An API for virtualenv and pip. * [pew](https://pypi.python.org/pypi/pew/) - A set of tools to manage multiple virtual environments. * [Vex](https://github.com/sashahart/vex) - Run a command in the named virtualenv. * [PyRun](https://www.egenix.com/products/python/PyRun/) - A one-file, no-installation-needed version of Python. -* [virtualenv-api](https://github.com/sjkingo/virtualenv-api) - An API for virtualenv/pip. ## Package Management @@ -124,10 +124,10 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [cx-Freeze](http://cx-freeze.readthedocs.org/) - Freezes Python scripts (cross-platform). * [py2exe](http://www.py2exe.org/) - Freezes Python scripts (Windows). +* [pynsist](http://pynsist.readthedocs.org/) - A tool to build Windows installers, installers bundle Python itself. * [py2app](http://pythonhosted.org/py2app/) - Freezes Python scripts (Mac OS X). * [PyInstaller](http://www.pyinstaller.org/) - Converts Python programs into stand-alone executables (cross-platform). * [dh-virtualenv](http://dh-virtualenv.readthedocs.org/) - Build and distribute a virtualenv as a Debian package. -* [pynsist](http://pynsist.readthedocs.org/en/latest/) - build a full Windows installers.Installer will work even for people without python. ## Build Tools @@ -216,6 +216,8 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [Mistune](https://github.com/lepture/mistune) - Fastest and full featured pure Python parsers of Markdown. * YAML * [PyYAML](http://pyyaml.org/) - YAML implementations for Python. +* Archive + * [unp](https://github.com/mitsuhiko/unp) - A command line tool that can unpack archives easily. ## Natural Language Processing @@ -727,7 +729,7 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [cryptography](https://cryptography.io/) - A package designed to expose cryptographic primitives and recipes to Python developers. * [PyNacl](https://github.com/pyca/pynacl) - Python binding to the Networking and Cryptography (NaCl) library. * [hashids](https://github.com/davidaurelio/hashids-python) - Implementation of [hashids](http://hashids.org) in Python. -* [Passlib](https://pythonhosted.org/passlib/index.html) - Secure password storage/hashing library, very high level +* [Passlib](https://pythonhosted.org/passlib/) - Secure password storage/hashing library, very high level. ## GUI @@ -844,7 +846,7 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [statsmodels](https://github.com/statsmodels/statsmodels) - Statistical modeling and econometrics in Python. * [astropy](http://www.astropy.org/) - A community Python library for Astronomy. * [orange](http://orange.biolab.si/) - Data mining, data visualization, analysis and machine learning through visual programming or Python scripting. -* [RDKit](http://www.rdkit.org/) - Cheminformatics and Machine Learning Software. +* [RDKit](http://www.rdkit.org/) - Cheminformatics and Machine Learning Software. * [Open Babel](http://openbabel.org/wiki/Main_Page) - A chemical toolbox designed to speak the many languages of chemical data. * [cclib](http://cclib.github.io/) - A library for parsing and interpreting the results of computational chemistry packages. * [Biopython](http://biopython.org/wiki/Main_Page) - Biopython is a set of freely available tools for biological computation. @@ -1003,7 +1005,6 @@ A curated list of awesome Python frameworks, libraries and software. Inspired by * [pluginbase](https://github.com/mitsuhiko/pluginbase) - A simple but flexible plugin system for Python. * [itsdangerous](https://github.com/mitsuhiko/itsdangerous) - Various helpers to pass trusted data to untrusted environments. * [blinker](https://github.com/jek/blinker) - A fast Python in-process signal/event dispatching system. -* [unp](https://github.com/mitsuhiko/unp) - Unpacks things ## Algorithms and Design Patterns