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Research Software Engineering
with Python
Research Software Engineering
with Python
Building software that makes research
possible
Damien Irving
Kate Hertweck
Luke Johnston
Joel Ostblom
Charlotte Wickham
Greg Wilson
First edition published 2022
by CRC Press
6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742
© 2022 Damien Irving, Kate Hertweck, Luke Johnston, Joel Ostblom, Charlotte Wickham, and
Greg Wilson
Reasonable efforts have been made to publish reliable data and information, but the author and
publisher cannot assume responsibility for the validity of all materials or the consequences of their
use. The authors and publishers have attempted to trace the copyright holders of all material
reproduced in this publication and apologize to copyright holders if permission to publish in this
form has not been obtained. If any copyright material has not been acknowledged please write and
let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced,
transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or
hereafter invented, including photocopying, microfilming, and recording, or in any information
storage or retrieval system, without written permission from the publishers.
For permission to photocopy or use material electronically from this work, access
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Danvers, MA 01923, 978-750-8400. For works that are not available on CCC please contact
mpkbookspermissions@tandf.co.uk
Trademark notice: Product or corporate names may be trademarks or registered trademarks and are
used only for identification and explanation without intent to infringe.
DOI: 10.1201/9781003143482
Publisher's note: This book has been prepared from camera-ready copy provided by the authors.
To David Flanders
who taught me so much about growing and sustaining coding communities.
— Damien
To Joshua.
— Charlotte
To Brent Gorda
without whom none of this would have happened.
— Greg
All royalties from this book are being donated to The Carpentries,
an organization that teaches foundational coding and data science skills
to researchers worldwide.
Contents
Welcome 1
0.1 The Big Picture . . . . . . . . . . . . . . . . . . . . . . . . . 1
0.2 Intended Audience . . . . . . . . . . . . . . . . . . . . . . . 2
0.3 What You Will Learn . . . . . . . . . . . . . . . . . . . . . . 3
0.4 Using this Book . . . . . . . . . . . . . . . . . . . . . . . . . 4
0.5 Contributing and Re-Use . . . . . . . . . . . . . . . . . . . . 4
0.6 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . 5
1 Getting Started 7
1.1 Project Structure . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2 Downloading the Data . . . . . . . . . . . . . . . . . . . . . 9
1.3 Installing the Software . . . . . . . . . . . . . . . . . . . . . 10
1.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.6 Key Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
iii
iv Contents
2.9 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.10 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.11 Key Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
15 Finale 369
15.1 Why We Wrote This Book . . . . . . . . . . . . . . . . . . . 370
Appendix 371
Contents ix
A Solutions 371
H YAML 481
I Anaconda 485
I.1 Package Management with conda . . . . . . . . . . . . . . . 485
I.2 Environment Management with conda . . . . . . . . . . . . 487
J Glossary 489
K References 503
Index 511
Other documents randomly have
different content
CHAPTER XV
DEMOCRACY AND DISTINCTION
Finally, all theories that aim to deduce from social conditions the
limits of personal achievement must be received with much caution.
It is the very nature of a virile sense of self to revolt from the usual
and the expected and pursue a lonesome road. Of course it must
have support, but it may find this in literature and imaginative
intercourse. So, in spite of everything, we have had in America men
of signal distinction—such, for instance, as Emerson, Thoreau and
Whitman—and we shall no doubt have more. We need fear no
dearth of inspiring issues; for if old ones disappear energetic minds
will always create new ones by making greater demands upon life.
The very fact that our time has so largely cast off all sorts of
structure is in one way favorable to enduring production, since it
means that we have fallen back upon human nature, upon that which
is permanent and essential, the adequate record of which is the chief
agent in giving life to any product of the mind.
FOOTNOTES:
[75] Democracy in America, vol. ii, book iv, chap. 7. But
elsewhere he expresses the opinion that this levelling and
confusion is only temporary. See, for example, book iii, chap. 21.
[76] Republic, book viii.
[77] Outre-Mer. English Translation, 306.
[78] See the final chapter of his French Traits.
[79] Conversation with Eckermann, May 12, 1825.
[80] French Traits, 385, 387, 393.
[81] Poe is the only notable exception that occurs to me.
[82] Memorials of Edward Burne-Jones, ii, 100, 101.
[83] Our most notable group of writers—flourishing at Concord
and Boston about 1850—is, of course, connected with the
maturing, in partial isolation, of a local type of culture, now
disintegrated and dispersed on the wider currents of the time.
[84] Outre-Mer, 25.
[85] In his essay on Balzac.
[86] Democracy in America, vol. ii, book i, chap. 10.
[87] Henry Van Brunt, Greek Lines, 225. Some of these
phrases, such as “illiterate combinations,” could never apply to
the work of good architects.
[88] Democracy in America, vol. ii, book i, chap. 11.
[89] Emerson, Alphonso of Castile.
CHAPTER XVI
THE TREND OF SENTIMENT