Planet SciPy
How to rename columns in Pandas Dataframe
pandas which simplifies doing these kind of data operations. 
First step is to install pandas package if it is not already installed. You can check if the package is installed on your machine by running
Deep Dive into TensorBoard: Tutorial With Examples
There is a common business saying that you can’t improve what you don’t measure. This is true in machine learning as well. […]
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Best Tools to Manage Machine Learning Projects
Managing Machine Learning Projects is not exactly a piece of cake but every data scientist already knows that. It touches many things: […]
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Performance of the Versioned HDF5 Library
In several industry and science applications, a filesystem-like storage model such as HDF5 is the more appropriate solution for manipulating large amounts of data. However, suppose that data changes over time. In that case, it's not obvious how to track those different versions, since HDF5 is a binary format and is not well suited for traditional version control systems and tools.
In a previous post, we introduced the Versioned HDF5 library, which implements a mechanism for storing binary data sets in a versioned way that feels natural to users of other version control systems, and described some of its features. In this post, we'll show some of the performance analysis we did while developing the library, hopefully making the case that reading and writing versioned HDF5 files can be done with a nice, intuitive API while being as efficient as possible. The tests presented here show that using the Versioned HDF5 library results in reduced disk space usage,
PyTorch-Ignite: training and evaluating neural networks flexibly and transparently
Read more… (28 min remaining to read)
This Week in Machine Learning: Diffbot the Web Crawler, AI Winter, 2021 Trends, & Google Maps
Algorithms and numbers are all around us, we just don’t realize how much they affects our daily lives. In our weekly roundup, […]
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Top 12 Machine Learning Podcasts That You Want to Check as a Data Scientist
As we know, education in this digital age is available in many forms like videos, PDFs, e-books, and podcasts. Podcasts have become […]
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Machine Learning Trends to Watch Out in 2020 and 2021
“Artificial intelligence will reach human levels by around 2029. Follow that out further to, say, 2045, and we will have multiplied the […]
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This Week in Machine Learning: Human-Machine Interaction, AI Limitations, and Neuralink
Machine learning and artificial intelligence help to discover new things, push the boundaries, and sometimes even save people’s lives. What can we […]
The post This Week in Machine Learning: Human-Machine Interaction, AI Limitations, and Neuralink appeared first on neptune.ai.
Implementing Content-Based Image Retrieval with Siamese Networks in PyTorch
Image retrieval is the task of finding images related to a given query. With content-based image retrieval, we refer to the task […]
The post Implementing Content-Based Image Retrieval with Siamese Networks in PyTorch appeared first on neptune.ai.
Traitlets - an introduction & use in Jupyter configuration management
You have probably seen Traitlets in applications, you likely even use it. The package has nearly 5 million downloads on conda-forge alone.
But, what is Traitlets ?In this post we'll answer this question along with where Traitlets came from, its applications, and a bit of history.
Read more… (8 min remaining to read)
Seqtembro de eventos virtuais e gratuitos sobre Qt e KDE
(Ok a piada com seqtembro funciona melhor na versão em inglês, seqtember, mas simbora) Por uma grande coincidência, obra do destino, ou nada disso, teremos um Setembro de 2020 repleto de eventos virtuais e gratuitos de alta qualidade sobre Qt e KDE. Começando de 4 à 11 do referido mês teremos o Akademy 2020, o… Continue a ler »Seqtembro de eventos virtuais e gratuitos sobre Qt e KDEIPython reproducible builds
Starting with IPython 7.16.1 (released in June 2020), you should be able to recreate the sdist (.tar.gz) and wheel
(.whl), and get byte for byte identical result to the wheels published on PyPI. This is a critical step toward being able
to trust your computing platforms, and a key component to improve efficiency of build and packaging platforms. It also
potentially impacts fast conda environment creation for users. The following goes into some reasons for why you should care.
Read more… (5 min remaining to read)
This Week in Machine Learning: ML Applications, Creative Revolution, and Fighting Pandemic
Every week brings tons of news, opinions, and discoveries in the world of machine learning and AI. But with our Weekly Roundup, […]
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Hyperparameter Tuning in Python: a Complete Guide 2020
Choosing the correct hyperparameters for machine learning or deep learning models is one of the best ways to extract the last juice […]
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Introducing Versioned HDF5
The problem of storing and manipulating large amounts of data is a challenge in many scientific computing and industry applications. One of the standard data models for this is HDF5, an open technology that implements a hierarchical structure (similar to a file-system structure) for storing large amounts of possibly heterogeneous data within a single file. Data in an HDF5 file is organized into groups and datasets; you can think about these as the folders and files in your local file system, respectively. You can also optionally store metadata associated with each item in a file, which makes this a self-describing and powerful data storage model.
Read more… (3 min remaining to read)
19 Best JupyterLab Extensions for Machine Learning
JupyterLab, a flagship project from Jupyter, is one of the most popular and impactful open-source projects in Data Science. One of the […]
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CARLsim5 Released!
IntroductionCARLsim5 is an efficient, easy-to-use, GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. It allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics using multiple off-the-shelf GPUs and x86 CPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level.
The present release, CARLsim 5, builds on the efficiency and scalability of earlier releases (Nageswaran et al., 2009; Richert et al., 2011, and Beyeler et al., 2015; Chou et al., 2018). The functionality of the simulator has been greatly expanded by the addition of a number of features that enable and simplify the creation, tuning, and simulation of complex networks with spatial structure.
New Features
pyCARL is a interface between the simulator-independent language PyNN and a CARLsim5 based back-end. In other words, you can write the code for a SNN model once, using the
(continued...)Improved workflows-as-applications: tips and tricks for building applications on top of snakemake
Writing applications around workflow systems, take 2.
Designing with and for developers
Open source is notorious for lack of design presence, enough so that my search to prove this fact has turned up nearly nothing. There’s many ways that such a gap in community might manifest, but one that I never anticipated was working with developers that had never interacted with a designer before.
A quick note for context: I’m writing this as a UX/UI designer working with open source projects for a little over a year. Because there are so many ways design processes can happen (enough to warrant its own blog post), this post is not intended to discuss design process deeply. My goal here is to pass on some of what I’ve learned that helps me design in this unusual space in hopes that it can help someone else. This post might seem most relevant for designers, but I think this experience could be helpful for developers as well.
Read more… (5 min remaining to read)
O que será do Lev com o “fim” da Saraiva?
Disclaimer: apesar do sobrenome, não tenho qualquer relação com a Saraiva. E também não tenho respostas para a pergunta do título. Como usuário do Lev acompanho com interesse a agonia da Saraiva. A rede de livrarias, uma das maiores do Brasil, está há anos em um imbróglio judicial devendo diversas editoras, em um processo que… Continue a ler »O que será do Lev com o “fim” da Saraiva?Dask Life Sciences Fellow [Open Job]
Dask is an open-source library for parallel computing in Python that interoperates with existing Python data science libraries like Numpy, Pandas, Scikit-Learn, and Jupyter. Dask is used today across many different scientific domains. Recently, we’ve observed an increase in use in a few life sciences applications: Large scale imaging in microscopy Single cell analysis Genomics […]
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STX Next, Python development company, uses Spyder to improve their workflow
STX Next, one of Europe's largest Python development companies, has shared with us how Spyder has been a powerful tool for them when performing data analysis. It is a pleasure for us on the Spyder team to work every day to improve the workflow of developers, scientists, engineers and data analysts. We are very glad to receive and share a STX Next testimonial about Spyder, along with an interview with one of their developers, Michael Wiśniewski, who has found Spyder very useful in his job.
In an era of a continuously growing demand for analysis of vast amounts of data, we are facing increasingly complex tasks to perform. Sure, we are not alone—there are many great tools designed for scientists and data analysts. We have NumPy, SciPy, Matplotlib, Pandas, and others. But, wouldn't it be nice to have one extra tool that could combine all the required packages into one compact working environment? Asking this question
(continued...)NumFOCUS Introduces New Supporter Program
Today NumFOCUS is pleased to introduce a new program for our individual supporters, called Open Science Champions. Each year, our community members generously support NumFOCUS and our Projects in several ways; this program is intended to connect these various forms of support so that we can engage with our community most effectively and offer our […]
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Educação Vigiada
Essa época de pandemia tem sido de produção em muitas frentes, o que infelizmente implica na redução de tempo para divulgação das mesmas aqui no blog. Nesse post quero me redimir dessa falta falando de um dos projetos que acho dos mais importantes que contribui recentemente, o Educação Vigiada. Há alguns meses o projeto Educação… Continue a ler »Educação VigiadaQuansight Labs: what I learned in my first 3 months
I joined Quansight at the beginning of April, splitting my time between PyTorch (as part of a larger Quansight team) and contributing to Quansight Labs supported community-driven projects in the Python scientific and data science software stack, primarily to NumPy. I have found my next home; the people, the projects, and the atmosphere are an all around win-win for me and (I hope) for the projects to which I contribute.
Read more… (2 min remaining to read)
Open Source Developer Advocate
Position Overview The primary role of the Open Source Developer Advocate is to represent and support developers of NumFOCUS open source projects by serving as a link to internal and external stakeholders as well as the global user community. You will generate attention and support by applying your technical knowledge, passion for open source data […]
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Learn NixOS by turning a Raspberry Pi into a Wireless Router
I recently moved, and my new place has a relatively small footprint. (Yes, I moved during the COVID-19 pandemic. And yes, it was crazy.) I quickly realized that was going to need a wireless router of some sort, or more formally, a wireless access point (WAP). Using my Ubuntu laptop's "wireless hotspot" capability was a nice temporary solution, but it had a few serious drawbacks.
Read more… (14 min remaining to read)
Engrenagem Ep. 04 – Aplicações KDE favoritas dos KDErs brasileiros
Nesse sábado dia 11/07 às 10h o KDE Brasil vai voltar com episódios do Engrenagem, o videocast da comunidade brasileira (que está há 4 anos sem episódios inéditos 🙂 ). Para retomar os trabalhos, o episódio trará 6 colaboradores brasileiros (Ângela, Aracele, Caio, Filipe (eu), Fred e Tomaz) falando de suas aplicações KDE favoritas –… Continue a ler »Engrenagem Ep. 04 – Aplicações KDE favoritas dos KDErs brasileirosWriting docs is not just writing docs
This blogpost was originally published on the Quansight Labs website.
I joined the Spyder team almost two years ago, and I never thought I was going to end up working on docs. Six months ago I started a project with CAM Gerlach and Carlos Cordoba to improve Spyder’s documentation. At first, I didn’t actually understand how important docs are for software, especially for open source projects. However, during all this time I’ve learned how documentation has a huge impact on the open-source community and I’ve been thankful to have been able to do this. But, from the beginning, I asked myself “why am I the ‘right person’ for this?”
Improving Spyder’s documentation started as part of a NumFOCUS Small Development Grant awarded at the end of last year. The goal of the project was not only to update the documentation for Spyder 4, but also to make it more user-friendly, so users can understand Spyder’s key concepts and
(continued...)Writing docs is not just writing docs
I joined the Spyder team almost two years ago, and I never thought I was going to end up working on docs. Six months ago I started a project with CAM Gerlach and Carlos Cordoba to improve Spyder’s documentation. At first, I didn’t actually understand how important docs are for software, especially for open source projects. However, during all this time I’ve learned how documentation has a huge impact on the open-source community and I’ve been thankful to have been able to do this. But, from the beginning, I asked myself “why am I the ‘right person’ for this?”
Read more… (3 min remaining to read)
Creating a Portable Python Environment from Imports
Python environments provide sandboxes in which packages can be added. Conda helps us deal with the requirements and dependencies of those packages. Occasionally we find ourselves working in a constrained remote machine which can make development challenging. Suppose we wanted to take our exact dev environment on the remote machine and recreate it on our local machine. While conda relieves the package dependency challenge, it can be hard to reproduce the exact same environment.
Read more… (3 min remaining to read)
Sobre o livro “Uma História de Desigualdade”
Finalizei a leitura do premiado livro do Pedro de Souza, “Uma História de Desigualdade – A Concentração de Renda entre os Ricos no Brasil 1926 – 2013“, baseado na tese que defendeu no programa de sociologia da UnB. É um livro de fôlego e que faz jus a todos os elogios que recebeu desde o… Continue a ler »Sobre o livro “Uma História de Desigualdade”Thanking the people behind Spyder 4
This blogpost was originally published on the Quansight Labs website.
After more than three years in development and more than 5000 commits from 60 authors around the world, Spyder 4 finally saw the light on December 5, 2019! I decided to wait until now to write a blogpost about it because shortly after the initial release, we found several critical performance issues and some regressions with respect to Spyder 3, most of which are fixed now in version 4.1.3, released on May 8th 2020.
This new release comes with a lengthy list of user-requested features aimed at providing an enhanced development experience at the level of top general-purpose editors and IDEs, while strengthening Spyder's specialized focus on scientific programming in Python. The interested reader can take a look at some of them in previous blog posts, and in detail in our Changelog. However, this post is not meant to describe those improvements, but to acknowledge all people that contributed
(continued...)Technical discussions are hard; a few tips
Note
This post discuss the difficulties of communicating while developing open-source projects and tries to gives some simple advice.
A large software project is above all a social exercise in which technical experts try to reach good decisions together, for instance on github pull requests. But communication is difficult, in …
Tidynamics, what use?
In 2018 I published small Python library, tidynamics. The scope was deliberately limited: compute the typical correlation functions for stochastic and molecular dynamics: the autocorrelation and the mean-square displacement. Two years later, I wonder about its usage.
Moderna, IMC Renew NumFOCUS Corporate Sponsorships
Monday, May 18th, 2020 Two NumFOCUS corporate supporters recently made fresh commitments to our open source mission. Trading firm IMC and biotechnology company Moderna Therapeutics each renewed their corporate sponsorships earlier this month. Both companies have supported NumFOCUS since 2018 at our Silver and Bronze sponsorship levels, respectively. Asked about his company’s decision to partner […]
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NumFOCUS Projects helping combat the COVID-19 pandemic
Open source tools are uniquely positioned to help combat the ongoing COVID-19 pandemic through their adaptable and collaborative nature. NumFOCUS sponsored and affiliated projects are being used on a global scale to meet the needs of researchers and data scientists. Our projects are being used in groundbreaking scientific efforts to create response models, visualize and […]
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Lazy River of Curious Content 0
This is the first post of what I'm calling a Lazy
River of Curious Content.
This is a way to review stuff that I've been doing, dealing with, or find
interesting during the week recently (This was
originally written two weeks ago, May 3rd, my shoddy internet connectivity kept
me from posting it.). I'm loosely following the format that Justin Sherrill
uses with great effect over at
https://dragonflydigest.com
Learn NixOS by turning a Raspberry Pi into a Wireless Router Friend of the show, Anthony Scopatz, tried NixOS for the first time and provides a detailed report:
"While I had read the NixOS pamphlets, and listened politely when the faithful came knocking on my door at inconvenient times, I had never walked the path of functional Linux enlightenment myself"
Reading through that made me file away a todo of writing up how I use propellor (and why). But those todo sometimes just pile up for a while...
An interview of one of my long time nerd-crushes, Rob Pike. The questions focus on the Go programming
(continued...)sourmash databases as zip files, in sourmash v3.3.0
Use compressed databases directly!
LaKademy 2019
Em novembro passado, colaboradores latinoamericanos do KDE desembarcaram em Salvador/Brasil para participarem de mais uma edição do LaKademy – o Latin American Akademy. Aquela foi a sétima edição do evento (ou oitava, se você contar o Akademy-BR como o primeiro LaKademy) e a segunda com Salvador como a cidade que hospedou o evento. Sem problemas… Continue a ler »LaKademy 2019Akademy 2019
Em setembro de 2019 a cidade italiana de Milão sediou o principal encontro mundial dos colaboradores do KDE – o Akademy, onde membros de diferentes áreas como tradutores, desenvolvedores, artistas, pessoal de promo e mais se reúnem por alguns dias para pensar e construir o futuro dos projetos e comunidade(s) do KDE Antes de chegar… Continue a ler »Akademy 2019Yellowbrick Update – April 2020
Yellowbrick released Version 1.1 on February 25, 2020. If you haven’t yet upgraded simply type pip install yellowbrick -U or conda install -c districtdatalabs yellow-brick into your terminal/command prompt to get it. The major improvement in v1.1 is introducing quick methods or one-liners to generate your favorite ML plots more quickly with Yellowbrick. Dr. Rebecca […]
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2020 PyData Conferences Update [COVID-19]
We wanted to give an update to our community regarding the upcoming 2020 PyData conferences. We have been closely monitoring the situation and to help ensure the safety of our community given the threat of the COVID-19 virus, the following in-person events have been postponed to 2021: PyData Miami PyData Amsterdam PyData LA PyData London PyData […]
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Scientific Software Developer- Contract Basis [SunPy Project]
Scientific Software Developer- Contract Basis NumFOCUS is seeking a Scientific Software Developer to support the SunPy project. SunPy is a Python-based open source scientific software package supporting solar physics data analysis. This is a 1 year contract. The successful applicant will work to improve SunPy’s functionality. There are four main tasks: Report on […]
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Creating the ultimate terminal experience in Spyder 4 with Spyder-Terminal
This blogpost was originally published on the Quansight Labs website.
The Spyder-Terminal project is revitalized! The new 0.3.0 version adds numerous features that improve the user experience, and enhances compatibility with the latest Spyder 4 release, in part thanks to the improvements made in the xterm.js project.
First, we were able to update all the old JavaScript files to use ES6/JSX syntax and the tests for the client terminal. This change simplified the code base and maintenance and allows us to easily extend the project to new functionalities that the xterm.js API offers. In order to compile this code and run it inside Spyder, we migrated our deployment to Webpack.
Multiple shells per operating systemIn the new release, you now have the ability to configure which shell to use in the terminal. On Linux and UNIX systems, bash, sh, ksh, zsh, csh, pwsh, tcsh, screen, tmux, dash and rbash are supported, while cmd and powershell are the
Software and workflow development practices (April 2020 update)
How we develop software and workflows in the DIB Lab, in 2020.
LaKademy 2019
Past November 2019 KDE fellows from Latin-America arrived in Salvador – Brazil to attend an one more edition of LaKademy – the Latin American Akademy. That was the 7th edition of the event (or the 8th, if you count Akademy-BR as the first LaKademy) and the second one with Salvador as host city. No problem… Continue a ler »LaKademy 2019Is it getting better yet? An optimistic visual guide to the Coronavirus pandemic
As the apocalypse rumbles on, I found myself wondering "Is it getting any better?"
Daily updates of spiralling case numbers (and worse, deaths) does little to give a sense of whether we're getting to, or already past, the worst of it.
To answer that question for myself and you, I …
On the Link Between Polynomials and Optimization
There's a fascinating link between minimization of quadratic functions and polynomials. A link that goes deep and allows to phrase optimization problems in the language of polynomials and vice versa. Using this connection, we can tap into centuries of research in the theory of polynomials and shed new light on …
pheriday 3: infrastructure
Looks like we can't inline audio for your browser. That's cool, just find the direct file links below.
paul's habitual errant ramblings (on Fr)idays
pheridays: 3
2020-04-10: A week ago, I recorded a 5 minute audio segment of some stuff I've been thinking about, but when I started to write it up I stumbled into and kept dropping down a deep technostalgic hole.
fall down along with me:
https://pirsquared.org/blog/pheriday-infrastructure.html
The recording is just shy of five minutes long, you can also download it in different formats, depending on your needs, if the audio tag above doesn't suit you:
https://pirsquared.org/pheridays/2020-04-03.ogg
(2.9 Mb)
https://pirsquared.org/pheridays/2020-04-03.mp3
(4.5 Mb)
https://pirsquared.org/pheridays/2020-04-03.m4a
(6.3 Mb)
--
Stuff I mentioned in the audio:
Propellor - "configuration management system using Haskell and Git" by Joey Hess
OpenWRT - specifically - reducing Bufferbloat
Mumble - "a free, open source, low latency, high quality voice chat application."
sourcehut.org - "the hacker's forge" also know as sr.ht by Drew DeVault
Jitsi - "Multi-platform open-source video conferencing"
OpenFire - "real time collaboration (RTC) server licensed under the
(continued...)PyData COVID-19 Response
The safety and well-being of our community are extremely important to us. We have therefore decided to postpone all PyData conferences scheduled to take place until the end of June: PyData Miami PyData London PyData Amsterdam We have been closely monitoring the situation and believe this is the best action to take based on the […]
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Statement on Coronavirus
As you are aware, the Coronavirus (COVID-19) is a topic of frequent and ongoing discussions. We would like to provide an update on our status and policies as well as provide resources for additional information. As of today, our event schedule remains as posted on event sites. Any changes or updates will be immediately shared. […]
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Some snakemake hacks for dealing with large collections of files
snakemake4life
Akademy 2019
Past September the Italian city of Milan hosted the KDE contributors meeting called Akademy, the main KDE conference where contributors from different areas like translators, developers, artists, promoters and more stay together for some days thinking and building the future of KDE projects and community(ies). Firstly before Akademy I departed from Brazil to Portugal to… Continue a ler »Akademy 2019Announcing JupyterCon 2020
NumFOCUS is excited to be a part of JupyterCon 2020. JupyterCon will be held August 10 – 14 in Berlin, Germany at the Berlin Conference Center. We invite you to participate in this exciting community event! Read the full announcement here. JupyterCon 2020 is an event brought to you in partnership by Project Jupyter and NumFOCUS.
The post Announcing JupyterCon 2020 appeared first on NumFOCUS.
MDAnalysis joins NumFOCUS Sponsored Projects
NumFOCUS is pleased to announce the newest addition to our fiscally sponsored projects: MDAnalysis MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written […]
The post MDAnalysis joins NumFOCUS Sponsored Projects appeared first on NumFOCUS.
Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.
Using k-mers and taxonomy to find contamination in metagenomes
Advancing research software in the UK through an SSI fellowship
I have been selected as part of the 2020 cohort of Fellows of the Software Sustainability Institute!
The Institute cultivates world-class research with software. It's based at the universities of Edinburgh, Manchester, Southampton, and Oxford in the UK. Their motto says it all:
The SSI has a yearly fellowship program to fund the organization of communities around scientific software (creating of local user groups, workshops, hackathons, etc). Even more importantly, they organize several events to get current and past fellows in the same place doing awesome stuff. I'm really looking forward to this year's Collaborations Workshop (registration is open to all, not just fellows). I applied at the end of last year and was selected to join the 2020 cohort of fellows along with some truly amazing people.
My plan for the fellowship is to
(continued...)Don't fund Software that doesn't exist
sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes
Using k-mers and taxonomy to find contamination in metagenomes
Finding problematic bacterial/archaeal genomes using k-mers and taxonomy
Some things in Genbank look ...odd.
How does sourmash's lca classification routine compare with GTDB classifications?
GTDB databases again!
Sourmash LCA databases now available for the GTDB taxonomy
GTDB databases!
Two PhD studentships at the University of Liverpool
I have two open positions for funded studentships at the University of Liverpool. Applications are open until 10 January 2020.
Project descriptionsFollow the links for more detailed versions.
Bringing machine learning techniques to geophysical data processing
The goal of this project is to investigate the use of existing machine learning techniques to process gravity and magnetics data using the Equivalent Layer Method. The methods and software developed during this project can be applied to process large amounts of gravity and magnetics data, including airborne and satellite surveys, and produce data products that can enable further scientific investigations. Examples of such data products include global gravity gradient grids from GOCE satellite measurements, regional magnetic grids for the UK, gravity grids for the Moon and Mars, etc.
Large-scale mapping of the thickness of the
(continued...)Getting a big scientific prize for open-source software
Note
An important acknowledgement for a different view of doing science: open, collaborative, and more than a proof of concept.
A few days ago, Loïc Estève, Alexandre Gramfort, Olivier Grisel, Bertrand Thirion, and myself received the “Académie des Sciences Inria prize for transfer”, for our contributions to the scikit-learn project …
Variable Explorer improvements in Spyder 4
This blogpost was originally published on the Quansight Labs website.
Spyder 4 will be released very soon with lots of interesting new features that you'll want to check out, reflecting years of effort by the team to improve the user experience. In this post, we will be talking about the improvements made to the Variable Explorer.
These include the brand new Object Explorer for inspecting arbitrary Python variables, full support for MultiIndex dataframes with multiple dimensions, and the ability to filter and search for variables by name and type, and much more.
It is important to mention that several of the above improvements were made possible through integrating the work of two other projects. Code from gtabview was used to implement the multi-dimensional Pandas indexes, while objbrowser was the foundation of the new Object Explorer.
New viewer for arbitrary Python objectsFor Spyder 4 we added a long-requested feature: full support for inspecting any kind of Python object through the Variable
(continued...)File management improvements in Spyder 4
This blogpost was originally published on the Quansight Labs website.
Version 4.0 of Spyder is almost ready! It has been in the making for well over two years, and it contains lots of interesting new features. We will focus on the Files pane in this post, where we've made several improvements to the interface and file management tools.
Simplified interfaceIn order to simplify the Files pane's interface, the columns corresponding to size and kind are hidden by default. To change which columns are shown, use the top-right pane menu or right-click the header directly.
First, we added the ability to associate different external applications with specific file extensions they can open. Under the File associations tab of the Files preferences pane, you can add file types and set the external program used to open each of them by default.
Once you've set this up, files will automatically launch in the associated application when opened from the Files pane in Spyder.
(continued...)This Week in Glean: November 1, 2019
When data goes wrong
Loan Amortisation Schedule using R and Python
When you take a loan from bank at x% annual interest rate for N number of years. Bank calculates monthly (or quarterly) instalments based on the following factors :
- Loan Amount
- Annual Interest Rate
- Number of payments per year
- Number of years for loan to be repaid in instalments
Introducing napari: a fast n-dimensional image viewer in Python
I'm really excited to finally, officially, share a new(ish) project called napari with the world. We have been developing napari in the open from the very first commit, but we didn't want to make any premature fanfare about it… Until now. It's still alpha software, but for months now, both the core napari team and a few collaborators/early adopters have been using napari in our daily work. I've found it life-changing.
The backgroundI've been looking for a great nD volume viewer in Python for the better part of
a decade. In 2009, I joined Mitya Chklovskii's lab and the FlyEM team at the
Janelia [Farm] Research Campus to work on the segmentation of 3D electron
microscopy (EM) volumes. I started out in Matlab, but moved to Python pretty
quickly and it was a very smooth transition (highly recommended! ;). Looking at
my data was always annoying though. I was either looking at single 2D slices
using matplotlib.pyplot.imshow, or saving the volumes in VTK format and
loading them into ITK-SNAP — which worked ok
O SERPRO e a validação de documentos digitais
No rascunho do post anterior sobre os documentos digitais no Brasil acabei escrevendo bastante sobre o papel do SERPRO nesse processo – tanto que decidi separá-lo em um post próprio. Com o lançamento do e-Título foi necessário para o TSE criar uma maneira de validar o documento digital para evitar fraudes. A tecnologia adotada foi… Continue a ler »O SERPRO e a validação de documentos digitaisHow to Evaluate the Logistic Loss and not NaN trying
A naive implementation of the logistic regression loss can results in numerical indeterminacy even for moderate values. This post takes a closer look into the source of these instabilities and discusses more robust Python implementations.
Uvas Gold 200
My poem about a rainy 200k was published in the Fall 2019 issue of American Randonneur (a quarterly magazine published by Randonneurs USA)
I've been doing samizdat poetry for as long as I've had a web presence (since 1999), but I am now officially a published poet! (I am deliberately not counting the embarrasing hackjob that was published in a youth anthology when I was in 8th grade.)
You can find "Uvas Gold 200" on page 26 - either directly on this skeuomorphic leafing viewer or the PDF, but I'm republishing both the exposition blurb and the poem below. If you prefer to listen, I recorded a reading of it that you can download in different flavors: a local audio only, a local video, or the embeded video version below.
(continued...)Uvas Gold 200k starts and ends in Fremont, CA and was held on Saturday, December 1st, 2018. The ride frontloads the climbing by going nearly half-way up Mount
Spyder 4.0: Kite integration is here
This blogpost was originally published on the Quansight Labs website.
Note: Kite is sponsoring the work discussed in this blog post, and in addition supports Spyder 4.0 development through a Quansight Labs Community Work Order.
As part of our next release, we are proud to announce an additional completion client for Spyder, Kite. Kite is a novel completion client that uses Machine Learning techniques to find and predict the best autocompletion for a given text. Additionally, it collects improved documentation for compiled packages, e.g. Matplotlib, NumPy and SciPy, that cannot be obtained easily by using traditional code analysis packages such as Jedi. Although Kite is not open source like Spyder, you can download it without charge at the Kite website.
By incorporating Kite into Spyder, we will improve and provide the ultimate autocompletion and signature retrieval experience for most of the scientific Python stack and beyond. For instance, let’s take a look at the following PyTorch completion. While
(continued...)An initial report on the Common Fund Data Ecosystem
Helping DCCs get FAIRer
Object Oriented Programming in Python : Learn by Examples
In the above example, car is an object. Functions are called methods in OOP world. Characteristics are attributes (properties). Technically attributes are variables or values related to the state of the object whereas methods
Precision Recall Curve Simplified
Comparing two genome binnings quickly with sourmash
Comparing two sets of MAGs, for fun and profit!
Calculate KS Statistic with Python
In data science, it compares the cumulative distribution of events and non-events and KS is where there is a maximum difference between the two distributions. In simple words, it helps us to understand how well our predictive model is able to discriminate between events and
A Complete Guide to Python DateTime Functions
- datetime
- date
- time
- timedelta
People who have no experience of working with real-world datasets might have not encountered date columns. They might be under impression that working with dates is rarely used and not so
What are *args and **kwargs and How to use them
args is a short form of arguments. With the use of *args python takes any number of arguments in user-defined function and converts user inputs to a tuple named args. In other words, *args means zero or more arguments which are stored in a tuple named args. When you define function without *args, it has a fixed number of inputs which means it cannot accept more (or less) arguments than you defined in the function.
In the example code below, we are creating a very basic function which adds two numbers. At the same time, we created a
Python : 10 Ways to Filter Pandas DataFrame
- Select all the active customers whose accounts were opened
Python Dictionary Comprehension with Examples
- Keys : Think about columns in tables. It must be unique (like column names cannot be duplicate)
- Values : It is similar to rows in tables. It can be duplicate.
To extract keys, values and structure of dictionary, you can submit the following commands.
d = {'a': [1,2], 'b': [3,4], 'c': [5,6]}
d.keys() # 'a', 'b', 'c'
d.values() # [1, 2], [3, 4], [5,
HTML outputs in Jupyter
SummaryUser interaction in data science projects can be improved by adding a small amount of visual deisgn.
To motivate effort around visual design we show several simple-yet-useful examples. The code behind these examples is small and accessible to most Python developers, even if they don’t have much HTML experience.
This post in particular focuses on Jupyter’s ability to add HTML output to any object. This can either be full-fledged interactive widgets, or just rich static outputs like tables or diagrams. We hope that by showing examples here we will inspire some throughts in other projects.
This post was supported by replies to this tweet. The rest of this post is just examples.
IrisI originally decided to write this post after reading another blogpost from the UK Met office, where they included the HTML output of their library Iris in a a blogpost
(work by Peter Killick, post by Theo McCaie)
The fact that the output provided by an interactive session is the same output that you would provide in a published result helps everyone. The interactive
(continued...)Python list comprehension with Examples
f(x) = x2, f(x) will always return the same result with the same x value. The function has no "side-effect" which means an operation has no effect on a variable/object that is outside the intended usage. "Side-effect" refers to leaks in your code which can modify a mutable data structure or variable. Functional programming is also good for parallel computing as there is no
Don't cite the No Free Lunch Theorem
Tldr; You probably shouldn’t be citing the "No Free Lunch" Theorem by Wolpert. If you’ve cited it somewhere, you might have used it to support the wrong conclusion. What it actually (vaguely) says is “You can’t learn from data without making assumptions”.The paper on the “No Free Lunch Theorem”, actually called "The Lack of A Priori Distinctions Between Learning Algorithms" is one of these papers that are often cited and rarely read, and I hear many people in the ML community refer to it when supporting the claim that “one model can’t be the best at everything” or “one model won’t always be better than another model”. The point of this post is to convince you that this is not what the paper or theorem says (at least not the one usually cited by Wolpert), and you should not cite this theorem in this context; and also that common versions cited of the "No Free Lunch" Theorem (continued...)
15 ways to read CSV file with pandas
pip install pandas. Next step is to load the package by running the following command. pd is an alias of pandas package. We will use it instead of full name "pandas". import pandas as pd
Matplotlib Tutorial : Learn with Examples in 3 hours
MATLAB programming language and provides a similar MATLAB like interface for graphics. The beauty of this library is that it integrates well with pandas package which is used for data manipulation. With the combination of these two libraries, you can easily perform data wrangling along with visualization and get valuable insights out of data. Like ggplot2 library in R, matplotlib library is the grammar of graphics in Python and most used library for charts in Python. 
Write Short Blogposts
I encourage my colleagues to write blogposts more frequently. This is for a few reasons:
-
It informs your broader community what you’re up to, and allows that community to communicate back to you quickly.
You communicating to the community fosters a sense of collaboration, openness, and trust. You gain collaborators, build momentum behind your work, and curate a body of knowledge that early adopters can consume to become experts quickly.
Getting feedback from your community helps you to course-correct early in your work, and stops you from wasting time in inefficient courses of action.
You can only work for a long time without communicating if you are either entirely confident in what you’re doing, or reckless, or both.
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It increases your visibility, and so is good for your career.
I have a great job. I find my work to be both
How to encourage participation in teleconferences
Participation is good!
How to drop one or multiple columns from Pandas Dataframe
- Drop or Keep rows and columns
- Aggregate data by one or more columns
- Sort or reorder data
- Merge or append multiple dataframes
- String Functions to handle text data
- DateTime Functions to handle date or time format columns
import command. import pandas as pd
import numpy as np
df = pd.DataFrame(np.random.randn(6, 4), columns=list('ABCD'))
A B C D
0 -1.236438 -1.656038
String Functions in Python with Examples
The cost of an open source contribution
Open source is massively successful. Some say it’s eating the world, although to my ears that phrasing doesn’t sound entirely like a good thing. Open source maintainers are always in need of help, and over the past years I’ve seen a lot of focus on ways open source projects can grow their communities and gain new contributors. Guidance on how to go about finding new contributors is easily found. E.TDK-Micronas partners with Quansight to sponsor Spyder
This blogpost was originally published on the Quansight Labs website
TDK-Micronas is sponsoring Spyder development efforts through Quansight Labs. This will enable the development of some features that have been requested by our users, as well as new features that will help TDK develop custom Spyder plugins in order to complement their Automatic Test Equipment (ATE’s) in the development of their Application Specific Integrated Circuits (ASIC’s).
At this point it may be useful to clarify the relationship the role of Quansight Labs in Spyder's development and the relationship with TDK. To quote Ralf Gommers (director of Quansight Labs):
(continued...)"We're an R&D lab for open source development of core technologies around data science and scientific computing in Python. And focused on growing communities around those technologies. That's how I see it for Spyder as well: Quansight Labs enables developers to be employed to work on Spyder, and helps with connecting them to developers of other projects in similar situations. Labs should be an enabler to let the Spyder project, its community and individual developers grow.
Why citations are not enough for open source software
A few weeks ago I wrote about why you should cite open source tools. Although I think citations important, though, there are major problems in relying on them alone to support open source work.
The biggest problem is that papers describing a software library can only give credit to the contributors at the time that the paper was written. The preferred citation for the SciPy library is “Eric Jones, Travis Oliphant, Pearu Peterson, et al”, 2001. The “et al” is not an abbreviation here, but a fixed shorthand for all other contributors. Needless to say many, many people have contributed to the SciPy library since 2001 (GitHub counts 716 contributors as of this writing), and they are unable to get credit within the academic system for those contributions. (As an aside, Google counts about 1,200 citations to SciPy, which is a breathtaking undercounting of its value and influence, and reinforces my earlier point: cite open source software! Definitely don't use this post as an excuse not to cite it!!!)
Not surprisingly, we have had
Spyder 4.0 takes a big step closer with the release of Beta 2!
This blogpost was originally published on the Quansight Labs website
It has been almost two months since I joined Quansight in April, to start working on Spyder maintenance and development. So far, it has been a very exciting and rewarding journey under the guidance of long time Spyder maintainer Carlos Córdoba. This is the first of a series of blog posts we will be writing to showcase updates on the development of Spyder, new planned features and news on the road to Spyder 4.0 and beyond.
First off, I would like to give a warm welcome to Edgar Margffoy, who recently joined Quansight and will be working with the Spyder team to take its development even further. Edgar has been a core Spyder developer for more than two years now, and we are very excited to have his (almost) full-time commitment to the project.
Spyder 4.0 Beta 2 released!Since August 2018, when the first beta of the 4.x series was released, the Spyder development team has been
(continued...)The Role of a Maintainer
What are the expectations and best practices for maintainers of open source software libraries? How can we do this better?
This post frames the discussion and then follows with best practices based on my personal experience and opinions. I make no claim that these are correct.
Let us Assume External ResponsibilityFirst, the most common answer to this question is the following:
- Q: What are expectations on OSS maintainers?
- A: Nothing at all. They’re volunteers.
However, let’s assume for a moment that these maintainers are paid to maintain the project some modest amount, like 10 hours a week.
How can they best spend this time?
What is a Maintainer?Next, let’s disambiguate the role of developer, reviewer, and maintainer
-
Developers fix bugs and create features. They write code and docs and generally are agents of change in a software project. There are often many more developers than reviewers or maintainers.
-
Reviewers are known
Using GitHub for janky project reporting - some code
We scripted GitHub for lightweight project reporting