FLOSS for Science

Note : This interview was recorded in the summer of 2020. However, due to the pandemic we could not release the episode timely. Therefore, the current status of FSF and recent events are not discussed in this episode.

In episode 31, we interviewed Craig Topham from the Licensing and Compliance Team of the GNU Project about GNU software licenses. We started by discussing about his involvment in the compliance team at the Free Software Foundation (FSF) and what got him interested in the topic of free software. The portion of the interview centered around the GNU project with an emphasis on the GNU software licenses. We went through the GPL, LGPL, AGPL and GFDL licenses to explain some of their differences and why you may want to use one instead of another. We asked questions about the specificities of licensing your code in the context of scientific software and the issue with licenses proliferation. Some of the differences between the different versions of the GPL were presented later in the discussion to show the improvements brought in the version 3 in regard to the compliance and patent sections. We asked him about his take on the philosophical differences between GNU style licenses and the MIT/BSD licenses in regard to the debate between user and developper freedom. We followed by going through some myths surrounding the GNU licenses and a general discussion about freedom and privacy. We finished the interview with our usual quick questions.

In episode 30, we interviewed Todd Gamblin from the Lawrence Livermore National Laboratory about the Spack project. We discussed his current research project along with his involvement in Spack. We widely discussed the philosophy of Spack, some usage patterns, its capabilities for managing package management in HPC clusters as well as standalone computers and which operating systems it supports at the moment. Todd shared with us his opinion on the trend for containerized workloads to achieve reproducible science and why it may not be the goal we need to set. He highlighted for us the similarities and differences between EasyBuild and Spack as well as the origin of those differences. We finished the interview with our usual quick questions.

00:00:00 Intro music

00:00:17 Introduction

00:00:36 Introducing Todd Gamblin

00:00:58 His current research topics

00:01:23 Spack as official duties

00:01:43 Spack usage at Lawrence Livermore National Laboratory

00:02:01 Other research projects

00:02:47 Profiling in HPC

00:04:24 His role as leader of software packaging technology for the exascale computing project

00:04:58 One-minute elevator pitch for Spack

00:05:34 Spack's usage philosophy compared to other package managers

00:06:59 Installation from source code or binary?

00:07:28 Spack's usage in the top500 super computers

00:07:49 Geographical distribution of users

00:08:18 Number of packages in the repo and some examples

00:09:05 Managing computer clusters with Spack's automation capabilities

00:11:04 Module files in Spack

00:12:32 Syntax of a Spack package file

00:13:43 Configuration of compiler flags

00:15:00 Importing python libraries in the Spack files

00:15:48 The procedure to submit a package

00:16:27 Review process for new packages

00:17:34 Reasons for rejection of Spack packages

00:18:01 Operating systems supported by Spack

00:18:23 WSL and Spack

00:18:58 Restricting packages to certain hardware and software configurations

00:20:04 Build testing and nightly builds

00:21:28 Working with containers in a Spack environment

00:22:25 Deploying prebuilt containers

00:23:05 About the "universality" of containers

00:24:16 His opinion on containerized applications for reproducible science

00:26:17 Spack's log file to document reproducibility

00:27:13 Reproducing older results

00:28:10 Specifying requirements on compilers

00:30:39 Post-installation verification test

00:31:10 Using Spack on a standalone computer instead of HPC systems

00:32:56 Differences between EasyBuild and Spack

00:34:24 EasyBuild in the top500

00:34:49 Transitionning between EasyBuild and Spack

00:35:38 Other alternatives

00:36:23 Using EasyBuild and Spack on the same system

00:38:36 When did the project start?

00:39:53 External contributions to Spack

00:40:53 How many core developpers?

00:41:30 Organization of the community and governance model

00:43:06 Who decides which package is accepted in the repo?

00:44:38 Spack's choice of software license

00:47:09 Todd's vision about the importance of FLOSS for the openness of science

00:48:13 Possible negative impacts of FLOSS

00:48:58 Most notable recent scientific discovery

00:49:14 Favourite text processing tool

00:49:25 A topic in science about which he recently changed his mind about

00:49:58 Anything else we forgot to ask?

00:50:09 How to contact Todd

00:50:46 Conclusion

In episode 29, we interviewed Jason R Coombs from the setuptools project. We started with a discussion about his background and his interest for Python and other programming languages. Following that, we had a thorough discussion about setuptools. We covered topics such as how he got involved in the project, the nature and composition of a Python package, why packaging your code can be important even for small projects, the hidden complexity of binary packages in the Python Package Index and how to maintain compatibility between Python versions. We also had a brief segment about the security aspects of Python packages. He informed us about how you could start contributing to the project and where to discuss Python packaging. We then followed with a general discussion about FLOSS in science and the problem of long-term maintenance in academia. We concluded the interview with our usual quick questions.

00:00:00.000 Intro

00:00:23 Introducing Jason R. Coombs

00:01:28 The first programming languages he learned and how he got into Python

00:03:46 New interesting programming languages

00:05:07 His favourite past Python projects

00:06:53 His one minute elevator pitch for setuptools

00:08:00 The relation between setuptools, PIP and Anaconda

00:10:43 How he got involved with the setuptools project

00:14:43 What is a Python package ?

00:16:07 What can be included in a package?

00:16:36 At which point is it beneficial to create a package ?

00:18:04 Managing compatibility with multiple versions of Python

00:20:33 Advantages of packages for small projects

00:22:46 How much work is required to create a package ?

00:25:05 Files required to create a Python package

00:27:45 Licenses and readme for Python packages

00:30:51 The nature of distribution archives

00:31:27 Compatibility of binary archives

00:32:39 Eggs and wheel files

00:34:32 Dealing with non portable packages in the Python Package Index across multiple operating systems

00:37:49 Uploading packages to the Python Package Index

00:39:12 Review for broken or malicious code

00:40:08 Vulneraility from package removal in the Python Package Index

00:43:24 Package name collisions

00:45:13 How many packages are in the Python Package Index

00:45:25 Alternatives to the main Python Package Index

00:46:35 Other packaging tools

00:47:39 How many developpers are involved in the project

00:48:31 Communication channels and discussions about Python packaging

00:49:53 Openings for new contributors

00:50:59 Skills required to contribute

00:52:24 The challenge of long term maintenance of packages in academia

00:55:43 His vision about the importance of FLOSS for the openess of science

00:59:18 Disadvantage of using FLOSS

01:01:24 The most notable scientific discovery in recent years

01:02:13 Favourite text processing tool

01:03:23 A topic in science about which he recently changed his mind

01:04:50 Contact informations

01:05:23 Conclusion

In episode 28, we interviewed Leah Silen from the NumFocus organization. She introduced us to the goals and the mission of the organization. We then had a discussion about the different levels of support provided by the organization to its member projects. She informed us about the legal, financial, technological and logistical support that can be provided by NumFocus. Following that, we asked her about the revenue sources of the organization as well as the possible influence from the corporate sponsors over the decisions and governance of the organization. We also discussed of the requirements to become part of NumFocus including details about the application process. We had a brief discussion about the history of the project and the evolution of the scope of projects that are part of the organization. After discussing the governance of the organization, we concluded the interview with our usual questions.

00:00:00 Intro

00:00:18 Introducing Leah Silen

00:02:28 Goals and mission of NumFocus

00:03:06 Examples of supported projects

00:03:39 Status of sponsorded and affiliated projects

00:05:04 Advantages of one status over the other

00:05:48 Legal challenges for open source scientific projects

00:07:19 Financial support for scientific open source projects

00:10:13 Assistance to apply for external grants

00:11:01 Paying developers from outside of US?

00:11:43 Revenue sources for NumFocus

00:12:21 Levels of corporate sponshorships

00:13:14 The influence of corporate sponsors

00:13:56 Motivations of corporate sponsors

00:15:02 Some of the sponsors of the NumFocus organization

00:16:05 Technological support for projects

00:17:03 Events previously supported by the organization

00:18:09 The kind of support that can be provided for events

00:19:22 Requirements for new projects

00:21:10 Clarification about the meaning of being a scientific oriented project

00:23:11 Requirements about the team size and strong governance within projects

00:24:58 The application process

00:26:18 Duration of support

00:26:44 Timeframe to receive a response for an application

00:28:30 Feedback in the case of rejection

00:29:12 Are there downsides of becoming a part of NumFocus?

00:30:32 Additional administrative overhead?

00:32:01 Location of NumFocus staff members

00:33:00 Foudation of NumFocus and initial projects

00:34:05 Opening to projects outside of the Python ecosystem

00:34:54 Favourite project?

00:35:46 Initial role in NumFocus

00:36:53 Term duration for positions at the board of directors

00:37:24 Selection process for the board of directors

00:38:31 Leah's vision about FLOSS and its importance for the openness of science

00:39:04 Negative impacts of FLOSS

00:39:33 Most notable scientific discovery in recent years

00:39:59 Favourite text processing tool

00:40:37 A topic in science about which she changed her mind about

00:41:36 Anything else we forgot to ask about?

00:42:54 How to contact Leah Silen

00:43:14 Outro

In episode 27, we interviewed Ralf Gommers from the NumPy and SciPy projects. We started our discussion by talking about his past research experience as a physicist and his transition to open source software and programming. This led him to get involved in projects such as PyWavelets, NumPy and SciPy. Following that, we had a great discussion about NumPy, its many features, its target audience and its performance. We learned why NumPy is not included in Python's standard library and its overlap with Scipy. We also compared the combination of Matlab to NumPy and Python and how users could transition to this open source solution. We then had a brief discussion about SciPy and the features it provides. Ralf informed us of the positive results from Google's previous Summer of Code and Season of Docs participations. We discussed how to reach the project and the many kinds of contributions that they are looking for. We talked about the importance of FLOSS for science and attribution of research output. We finished the interview with our classic quick questions and a reflection from Ralf about the need for more sustainability in open source software development as volunteer effort may not be sufficient in the future.

00:00:00 Intro

00:00:18 Introduction

00:00:33 Introducing Ralf Gommers

00:02:05 Research during his PhD and and PostDoc

00:03:20 When he started to use open source tools

00:03:52 Learning to code

00:04:39 PyWavelets, another sideproject he likes

00:05:55 His elevator pitch for NumPy

00:06:55 Vector arrays in Python before NumPy

00:07:49 How he got involved in the NumPy project

00:10:13 Traget users for NumPy

00:11:36 NumPy as part of the standard library?

00:13:24 Features provided by NumPy

00:14:22 Major differences between Python built-in list and NumPy's array

00:16:01 Structured data

00:16:45 Why appending a row to an array is made hard

00:18:09 Multithreaded code with NumPy

00:19:48 Distributed array processing

00:20:50 GPU computation with Python and NumPy

00:22:16 Linear algebra functions in NumPy

00:23:25 Overlap between SciPy and NumPy for linear algebra

00:23:55 Python speed as an interpreted language

00:25:43 Python with NumPy compared to Matlab

00:28:07 How easy is the transition between Matlab and Python Numpy

00:29:26 Performance difference between Matlab and Python

00:31:00 Commercial applications of NumPy

00:32:15 Contributions from the industry ans incentives to contribute

00:34:10 Elevator pitch for SciPy

00:35:37 Overview of some of the submodules in SciPy

00:38:11 The size of the communities

00:39:33 Participation in Google Summer of Code

00:40:24 Participation in Google Season of Docs

00:41:48 Communication channels in the project

00:43:25 Where to ask for support?

00:44:48 Possible contributions

00:46:25 Skills usefull to contribute to the NumPy project

00:48:12 Identifying possible contributions

00:48:52 The importance of FLOSS for science

00:52:02 Possible negative impact of FLOSS on science

00:52:49 Crediting contributions in science

00:53:42 Most notable scientific discovery in recent years

00:54:49 His favourite text processing tool

00:55:30 Volunteer effort may not be sufficient anymore

00:56:58 Contact informations for Ralf Gommers

00:57:27 Outro

In episode 26, we interviewed Bhavani Ravi about the Python data analysis library pandas. After a brief introduction about her use of machine leaning models for pharmaceutical research, we talked extensively about pandas. She told us how much pandas is important for her everyday tasks and the strict quality standards of the project. We talked about the features provided by pandas and its compatibility with other Python libraries. We then discussed the importance of FLOSS in her industry and how they are contributing back to important projects. She share with us her experience as a first time contributor to pandas and how to find good first time issues for newcomers. We finished the interview with out usual quick questions.

00:00:17 Introduction

00:00:26 Introducing Bhavani Ravi

00:00:49 Using machine learning models for pharmaceutical research

00:02:46 How she got involed in the pandas project

00:04:29 Her elevator pitch for pandas

00:04:43 How she use pandas in her everyday job

00:05:24 What does pandas bring that is lacking in basic Python

00:06:53 Preparing data for machine learning algorithms

00:08:12 The performance of pandas

00:09:21 Data formats supported by pandas

00:11:03 Data structures provided by pandas

00:11:42 Data analysis tools provided by pandas

00:12:32 Using pandas data structures with scikit-learn

00:12:55 Plotting data from pandas

00:13:39 Transition to Python version 2

00:14:51 Commercial usage of pandas

00:15:16 Companies contributing back to pandas

00:16:02 Exposition of students to pandas

00:16:42 Tutorials to start with pandas

00:18:26 Python libraries dependencies of pandas

00:18:55 Main communication channels

00:19:44 Her experience contributing to pandas

00:21:14 Skills to contribute to the project

00:21:49 List of good first issues

00:22:21 Tasks for non-programmers

00:23:12 FLOSS and the industry

00:24:16 The most notable scientific discovery in recent years

00:24:33 Her favourite text processing tool

00:25:06 Anything else?

00:25:38 How to contact Bhavani

00:25:57 Outro

In episode 25, we interviewed Kurt Kremitzki about the paramatric 3D modelling tool FreeCAD. After discussing his previous experiences with CAD software and how he got involved in the FreeCAD project, we asked him about the current development status of the project before digging deeper into a few of the workbenches offered by FreeCAD. We also compared FreeCAD to LibreCAD and QCAD for applications only requiring 2D drawing instead of parametric 3D models and we discussed about compatibility with commercial CAD systems and standard exchange file formats. We were pleased to learn about the development status of a stable topological naming engine paving the way for the integration of an official assembly workbench in future releases. We then discussed about the spread of FreeCAD in companies and universities as well as ways to contribute to the FreeCAD project. We finished the interview with out usual quick questions and with a mention of their recent presentions at FOSDEM 2020.

00:00:18 Introducing Kurt Kremitzki

00:02:16 How he got involved with FreeCAD

00:03:22 His previous CAD experience before working on FreeCAD

00:04:35 One minute elevator pitch for FreeCAD

00:05:50 Current general development status of FreeCAD

00:07:12 BIM with FreeCAD

00:09:24 What are workbenches in FreeCAD?

00:10:46 Core FreeCAD workbenches

00:11:40 Technical drawing with FreeCAD

00:13:44 FEM libraries integrated within FreeCAD

00:16:15 Multiphysics simulations

00:18:16 Model updates recalculations

00:19:04 Technical drawings and annotations

00:19:49 FreeCAD for 2D CAD drawing vs other FLOSS alternatives

00:21:08 Compatibility with commercial CAD systems and standard exchange file formats

00:23:41 Performance of STEP files conversion

00:24:54 FreeCAD's native file format

00:25:44 Version control with FreeCAD

00:27:01 File formats that are supported by FreeCAD

00:29:16 Integration of Python in FreeCAD

00:30:56 Assemblies with FreeCAD

00:33:29 Stable topological naming

00:35:10 Manual approach for static assemblies

00:36:30 When to expect a stable assembly workbench

00:37:20 How to test assemblies right now

00:38:33 FreeCAD's software license

00:39:16 Companies using FreeCAD

00:39:42 Universities using FreeCAD

00:40:16 FreeCAD's use in science and citations of FreeCAD

00:42:29 How many people are involved in the project

00:43:04 Main communication channels

00:43:54 How to contribute to FreeCAD

00:45:45 Kurt's vision of FLOSS and its importance for the openness of science

00:47:13 Most notable scientific discovery in recent years

00:47:47 Favourite text processing tool

00:48:11 A topic he changed his mind about in science

00:48:28 FreeCAD at FOSDEM 2020

00:49:33 How to contact Kurt

00:49:54 Outro

In episode 24, we interviewed Simon Hettrick Professor at the University of Southampton in the UK. We started the discussion with him by asking about his transition from deveoppin high-power lasers to founding the research software engineers (RSE) association and how his experiences got him in his current position. We then discussed about the roles of RSE in research and how funding for RSE evolved over the past. The discussion went on about the RSE association, its growth over time, branches in other countries and local events. We discussed that the relation between FLOSS and more sustainable research software is not always clear and more work is needed in that area. After talking with him about the lack of sufficient preparation that students receives during their undergrad studies in regard to the tools needed to tackle research software development we finished with our usual quick questions.

00:00:00 Intro

00:00:18 Introduction and Simon Hettrick's presentation

00:00:56 His academic status at the University of Southampton

00:01:53 His transition from developping high power compact lasers to RSE

00:03:31 About his PhD and general comments about PhD defenses

00:04:21 Any relations between laser and his current research area?

00:07:57 1 minute elevator pitch for UK RSE

00:08:32 The growing importance of software and the effect on funding

00:14:03 Defining what is a RSE

00:17:35 How many RSE in UK?

00:18:20 The state of preparation of the research community for brexit

00:20:05 When was the RSE association founded?

00:20:16 How to become a member of RSE UK and the growth rate of the association

00:22:44 Other RSE branches

00:24:42 Relations between RSE associations

00:25:40 Regional RSE organizations and RSE groups

00:27:09 Local meetups groups

00:28:00 Crediting research software development

00:31:39 Is FLOSS the norm or the exception for RSE?

00:35:09 Does FLOSS helps providing better and more sustainable research software?

00:38:55 Curriculum for new researchers

00:43:50 The state of research software licensing

00:46:13 Most notable recent scientific discovery

00:48:13 His favourite text processing tool

00:48:58 A topic in science he changed his mind about

00:50:13 How to contact Simon

00:50:37 Conclusion

In episode 23, we interviewed Dan Quintana from the University of Oslo. We started the discussion with him by asking the link between all his subjects of interest and where R fits into his workflow. We then had an extensive discussion about R including his must have R packages and the synthpop package for generating synthetic datasets. We then widened the discussion and talked about the multiple facets of open science and reproducibility. Dan then talked about what he sees as one of the next big challenge of science. We finished the interview with our usual quick questions.

00:00:18 Introduction

00:00:39 Presentation of Dan Quintana

00:01:55 The links between his research interests

00:04:00 Where does R fits in his workflow

00:05:22 His 30 seconds elevator pitch for R

00:06:28 How difficult is it to switch from SPSS to R?

00:08:05 The best time to switch to R

00:08:40 JASP and Jamovi as a gateway to R

00:10:53 Standing on the shoulders of giants with R

00:12:15 R or Python?

00:14:00 Dan's must have R packages

00:15:59 Ressources to learn R

00:17:21 Introduction to synthetic datasets

00:21:54 Synthetic datasets for privacy and their limitations

00:24:52 How much time should be spent to publish datasets and code

00:26:58 Dan's view on open science practices

00:28:27 FLOSS and open science practices

00:30:49 The licence he uses for sharing code and data

00:32:06 Obtaining a DOI with the Open Science Framework

00:32:21 Journal of Open Source Software

00:34:15 The importance of publishing in open access journals

00:37:28 Publishig in open access journals and plan S

00:39:09 The lack of affordability for open access publishing

00:40:22 Preprints as a solution?

00:43:04 How to publish a perfectly reproducible paper

00:46:02 How to convince other scientists to share their data and code

00:46:42 The next big challenge of science

00:48:55 The most notable discovery in recent years

00:51:20 Favourite text processing tool

00:51:43 A topic in science he recently changed his mind about

00:52:49 Anything else?

00:53:34 How to contact Dan Quintana

00:53:56 Conclusion

In episode 22, we interviewed Robert Dodier from the Maxima project. After a brief introduction and a presentation of Robert's current uses for Maxima he introduced what is Maxima and what can be achieved with it. We discussed some core concepts of Maxima's language as well as how to access the documentation within the software to help users. Then discussion went on about the interesting origin story of Maxima and its origin as a tool for AI. We then talked about the current state of the project and how can someone provide help. As well as our usual quick questions, we had an interesting discussion about the social aspects within FLOSS and other self-organized projects.

00:00:17 Introduction

00:00:26 Presentation of Robert Dodier

00:02:01 The scope of Maxima and its application for Bayesian inferences

00:02:57 Why not use R or another programming language for Bayesian inferences?

00:05:03 When did he discover Maxima?

00:05:29 Maxima's core features stability since 2003

00:06:04 His 30 seconds elevator pitchfor Maxima

00:06:43 Reference manual and Maxima's documentation

00:07:52 Accessing Maxima's documentation

00:08:41 Comparison with Maple and Mathematica

00:10:50 The concept of "code equal data"?

00:12:54 Maxima's language complexity/simplicity

00:15:13 User interfaces for Maxima

00:16:24 Console interface for Maxima

00:17:12 Presentation of the resulting equations or results

00:17:46 Integrating Maxima and LaTeX

00:19:08 The origin story of Maxima

00:25:17 Licensing status before the relicensing to GPL

00:26:00 Maxima for undergrad students and researchers

00:28:33 Robert's contributions to the project and its self-organized structure

00:31:39 How many people are involved in the project

00:32:13 Communication channels for the project

00:32:52 Underlying technologies in Maxima

00:34:27 Ressources for newcomers

00:35:47 Robert's vision about FLOSS in science

00:36:26 Negative impacts of FLOSS on science

00:37:25 The most notable scientific discovery in recent years

00:39:22 Robert's favourite text processing tool

00:40:04 The social aspect of FLOSS

00:42:34 Anything else he wanted to share with us?

00:43:39 How to contact Robert

00:43:57 Outro