-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.qmd
1176 lines (608 loc) · 34.3 KB
/
index.qmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
---
title: "-Better software for Better research-<br>Introduction to the FAIR<sup>2</sup> for Research Software training Programme"
format:
revealjs:
theme: [dark, custom.scss]
slide-number: true
show-slide-number: speaker
author: "<br>**Romain Thomas**<br>[Head of Research Software Engineering](https://rse.shef.ac.uk/),<br> The University of Sheffield<br>[rse.shef.ac.uk](https://rse.shef.ac.uk)"
institute: "<br><strong>FAIR24RS training programme Kick-off Seminar</strong>, October 2024"
date: ""
footer: "**Access** to the slides: [here](https://fair2-for-research-software.github.io/Better_software_for_better_research/#/what-if-a-generation-of-research-stop-doing-this) - **Source** [Github repository]([email protected]:FAIR2-for-research-software/Better_software_for_better_research.git)"
from: markdown+emoji
css: style.css
---
## Useful Information:
::: {.columns}
::: {.column width="60%"}
- This talk is recorded.
- You can follow the slides :arrow_right::arrow_right: <br>
- Slides are available freely on github.
- Ask questions in the google chat. Thanks to Tamora James for the moderation. <br>
- Every [blue]() text is a hyperlink
:::
::: {.column width="40%"}
{fig-align="center"}
:::
:::
## Who am I? {.smaller}
- Name : Romain Thomas
- Role : Head of Research Software Engineering
- Previously : Staff Astronomer and Software Project manager at the Very Large Telescope (Chile)
- Released/Published a few modules/software:
- [dfitspy](https://joss.theoj.org/papers/10.21105/joss.01249)
- [SPARTAN](https://www.sciencedirect.com/science/article/pii/S2213133720300810?via%3Dihub)
- [SCUBA](https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11449/2560271/The-SCUBA-project---First-layer-of-quality-control/10.1117/12.2560271.full)
{.absolute top="350" left="300" width="800" height="250"}
## Who are we? The teams behind the programme {.smaller}
**Research Software Engineering**
::: {.columns}
::: {.column width="30%"}
{fig-align="center"}
:::
::: {.column width="70%"}
The Research Software Engineering team is composed of 13 members and <span style="color:red">**collaborates with researchers across the University in building research software**</span>. Areas of expertise within the group include: general software development, code optimisation and performance, reproducibility, GPU computing and Deep Learning, High Performance Computing, training, etc...
:::
:::
## Who are we? The teams behind the programme {.smaller}
**Data Analytics Service**
::: {.columns}
::: {.column width="30%"}
{.absolute top="300" left="10" width="300" height="90"}
:::
::: {.column width="70%"}
The Data Analytics Service (IT Services) supports research excellence at the University of Sheffield by bridging technical and analytical gaps through consultation, delivering training, and long-term collaboration with research teams. <span style="color:red">DAS supports researchers with reproducible data analysis, data visualisation, data engineering, machine learning, statistics, big data, research software, web design, and much more.</span>
:::
:::
## Who are we? The teams behind the programme {.smaller}
**Library's Scholarly Communications**
::: {.columns}
::: {.column width="30%"}
{.absolute top="300" left="10" width="300" height="60"}
:::
::: {.column width="70%"}
The Library's Scholarly Communications Team provides specialist services to support researchers at the University of Sheffield. They offer guidance on making your research outputs open access, and give <span style="color:red">support on good practice in research data management, copyright and licensing as well as open research more broadly.</span>
:::
:::
# Why FAIR?
# Why ~~FAIR~~?
# Why OPEN?
## Research is a continuous process
<span style="color:red">"The succession of researchers is comparable to a single person who learns indefinitely.</span><br>
<font size="4">*Pascal, Pensee, French Mathematician, Physicist, inventor, philosopher and theologian [1623-1662]*</font>
{.absolute top="250" left="750" width="300" height="350"}
::: incremental
- That's very old....
- But still very valid...
- And becomes much more difficult with the<br>complexity of modern research
:::
## Research creates knowledge…that is passed down{.smaller}
<span style="color:red">"Knowledge is humankind's most precious treasure. Everything that we accomplished has been done due to the capacity to create a transmissible heritage, which spares each new generation the task of starting from scratch."</span> <font size="4">*B. Sirbey, le grand homme qui apprend.* </font>
<br><br><br>
> If we are doing the research we are doing today, it is thanks to the work of previous generations that created the knowledge that we are using now.
## And that can be trusted...
::: {.columns}
::: {.column width="60%"}
::: incremental
- Research relies on the ability to trust what has been done before.
- This means that a result has been tested, verified and could be <span style="color:red">reproduced</span> :arrow_right::arrow_right:
- Tools and methods used for a particular result are known and shared…
:::
:::
::: {.column width="40%"}
<br>
<font size="2">[The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-fair.html) project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: [10.5281/zenodo.3332807](https://dx.doi.org/10.5281/zenodo.3332807)</font>
:::
:::
## What if a generation of researchers stop doing this?
::: {.columns}
::: {.column width="60%"}
::: incremental
- Tools and methods used for a particular results are <span style="color:red">NOT</span> known and shared…
- This means that a result can <span style="color:red">NOT</span> be tested and verified and can <span style="color:red">NOT</span> be reproduced.
- :arrow_right: It is harder to trust research
:::
:::
::: {.column width="40%"}
<font size="2">[The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-fair.html) project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: [10.5281/zenodo.3332807](https://dx.doi.org/10.5281/zenodo.3332807)</font>
:::
:::
## Are we far from reaching this situation?
::: {.columns}
::: {.column width="40%"}
<br>
<font size="2">[Source: Baker M., Nature, 2016](https://www.nature.com/articles/533452a)</font>
:::
::: {.column width="60%"}
::: {.r-stack}
::: incremental
- 90% said there is a crisis!
- More than 70% of researchers have tried and failed to reproduce another scientist's experiments…
- <span style="color:red">And more than half have failed to reproduce their own experiments.</span>
:::
{.fragment width="600" height="300"}
:::
:::
:::
# So how do we get better?
## Let's improve!
{fig-align="center"}
<font size="2">[Source: www.aalto.fi](https://www.aalto.fi/en/open-science-and-research/getting-started-with-reproducibility-in-research)</font>
# And why not start with your software?
## Let's start by a definition: What is a software?
<br>
<br>
"Source code files, algorithms, scripts, computational workflows and executables that were created during the research process or for a research purpose."
<font size="4">[Barker et al. Scientific Data 9:622 (2022) “Introducing the FAIR Principles for research software”](https://dx.doi.org/10.1038/s41597-022-01710-x) </font>
# What is FAIR?
## The FAIR principles
::: {.columns}
::: {.column width="65%"}
{fig-align="center"}<br>
<font size="2">[The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-fair.html) project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: [10.5281/zenodo.3332807](https://dx.doi.org/10.5281/zenodo.3332807)</font>
:::
::: {.column width="35%"}
<br><br>
A guideline for those wishing to enhance the reusability of their data holdings<br><font size="4"> [–Wilkinson et al. (2016)–](https://www.nature.com/articles/sdata201618) </font>
:::
:::
## The FAIR principles
<br>
“Many of the FAIR Guiding Principles can be directly applied to research software by treating software and data as similar digital research objects. However, <span style="color:red">specific characteristics of software — such as its executability, composite nature, and continuous evolution and versioning</span> — make it necessary to revise and extend the principles.”
<font size="4">[Chue Hong, Neil P. et al, FAIR Principles for Research Software (FAIR4RS Principles)](https://doi.org/10.15497/RDA00068)</font>
## The FAIR principles: what do they say?
<br>
- <span style="color:red">Findable</span>: Software, and its associated metadata, is easy for both humans and machines to find
- <span style="color:red">Accessible</span>: Software, and its metadata, is retrievable via standardised protocols
<font size=4>[Barker *et al.* *Scientific Data* 9:622 (2022) "Introducing the FAIR Principles for research software" DOI: 10.1038/s41597-022-01710-x](https://dx.doi.org/10.1038/s41597-022-01710-x)</font>
::: {.notes}
FINDABLE: Research software should have a globally unique and persistent identifier (e.g., DOI or a persistent URL) so that it can be easily found and cited. Sufficient metadata should be provided to help users discover the software. This includes descriptions of the software's function, version information, authorship, and where to access it. The software and its metadata should be indexed in searchable repositories so it can be discovered via common search engines and research infrastructure platforms (e.g., Zenodo, GitHub, or institutional repositories).
ACCESSIBLE: The software should be easily retrievable using the unique identifier. Typically, this involves storing the software in a trusted repository that ensures long-term access. Clear information about the conditions under which the software can be accessed should be available, including open access options, if applicable. This ensures users understand whether they can freely use or adapt the software.
:::
## The FAIR principles: what do they say?
<br>
- <span style="color:red">Interoperable</span>: Software interoperates with other software by exchanging data and/or metadata, and/or through interaction via application programming interfaces (APIs), described through standards.
- <span style="color:red">Reusable</span>: Software is both usable (can be executed) and reusable (can be understood, modified, built upon, or incorporated into other software)
<font size=4>[Barker *et al.* *Scientific Data* 9:622 (2022) "Introducing the FAIR Principles for research software" DOI: 10.1038/s41597-022-01710-x](https://dx.doi.org/10.1038/s41597-022-01710-x)</font>
::: {.notes}
INTEROPERABLE: The software should use standardized data formats and interfaces where possible, allowing it to work with other software, tools, or systems. Clear documentation should be provided so users know how to integrate the software with other tools or systems. Where possible, the software should implement and support established protocols, formats, and APIs that are widely adopted in the research community.
REUSABLE: The software should be well-documented, including clear instructions on how to install, run, and modify it. The metadata should describe how and where the software can be reused, including dependencies, versioning, and requirements. An appropriate open or permissive license should be provided to ensure that others can legally reuse, modify, and redistribute the software. Adhering to coding standards, including the use of tests and continuous integration (CI), enhances the reliability and reusability of the software.
:::
## University's position about FAIR {.smaller}
<br>
‘‘We aspire to open research culture that values a diverse range of contributions and adheres to the FAIR principles to enable the results of our research to be of maximum benefit to society (findable, accessible, interoperable and reusable), whilst also respecting circumstances that limit data sharing (for example, due to issues of privacy, non-consent, contractual agreements, legislation or practicality).’’
[University of Sheffield, Statement on Open Research](https://www.sheffield.ac.uk/openresearch/university-statement-open-research)
<br><br>
‘‘All researchers, including postgraduate research students, have a personal responsibility to manage effectively the data they create….. All researchers are expected to document research data and software in line with the FAIR principles…..’’
[University of Sheffield, Policy on good research and innovation practices](https://www.sheffield.ac.uk/media/18953/download)
## Barriers to FAIR<sup>2</sup>4RS {.smaller}
::: {.columns}
::: {.column width="50%"}
::: {.incremental}
+ fear of prejudice
+ important to create a positive culture
+ fear of 'theft'
+ licensing and citation
+ technical and time barriers
+ support is available!
+ only need to learn once
+ non-commercialisable?
+ open source and commercialisation are compatible
+ greater impact through open source
:::
:::
::: {.column width="50%"}
<font size=3>[Better Science through Better Data 2017) scribe images.](https://doi.org/10.6084/m9.figshare.5558653.v1)</font>
:::
:::
## Benefits of FAIR<sup>2</sup>4RS
::: {.columns}
::: {.column width="50%"}
<font size=3>[Better Science through Better Data 2017) scribe images.](https://doi.org/10.6084/m9.figshare.5558653.v1)</font>
:::
::: {.column width="50%"}
::: {.incremental}
+ Accelerate research
+ Increase transparency of research
+ Increase visibility, citation, reputation and impact
+ Reduce duplication of effort
:::
:::
:::
## How to be FAIR?
{fig-align="center" width="800" height="500"}
## FA<span style="color:red">IR</span>4RS: Think about how you are coding...
::: {.columns}
::: {.column width="50%"}
::: incremental
- Where possible, make your code modular.
- Comment your code to make it as clear as possible.
- Create and provide tests that others can use.
- Follow code standards
:::
:::
::: {.column width="50%"}
<br>
{.absolute top="100" left="550" width="500" height="350"}
{.absolute top="330" left="510" width="400" height="150"}
{.absolute top="430" left="650" width="400" height="150"}
:::
:::
## FA<span style="color:red">IR</span>4RS: Be open even inside the code!{.smaller}
::: {.columns}
::: {.column width="50%"}
::: incremental
- Where possible and applicable, outputs (even between pieces of code) should use open and accessible data formats, which will help if other researchers only wish to use part of your code.
- <span style="color:red">But do NOT reinvent the wheel!</span> In some research fields data format are standardized :arrow_right: if you want people to use your code, use [your] community standards!
:::
:::
::: {.column width="50%"}
<br>
{.absolute top="150" left="550" width="500" height="350"}
:::
:::
## <span style="color:red">FAIR</span>4RS: Version your code!{.smaller}
::: {.columns}
::: {.column width="50%"}
::: incremental
- Using version control software platform such as Github/GitLab allows you to keep track of the changes you make to your code
- You can release version of your software/code/scripts directly from Github. While it should not be used a long term storage place, It gives a place where your code can be downloaded and where people can contribute.
:::
:::
::: {.column width="50%"}
{.absolute top="150" left="550" width="480" height="300"} <br><br><br><br><br><br><br><br><br><br>
<font size=2>[https://www.sheffield.ac.uk/library/research-data-management/repositories](https://www.sheffield.ac.uk/library/research-data-management/repositories)</font>
:::
:::
## FA<span style="color:red">IR</span>4RS: Document your code!{.smaller}
<br>
::: {.columns}
::: {.column width="50%"}
A little poem from [A beginner’s guide to writing documentation](https://www.writethedocs.org/guide/writing/beginners-guide-to-docs/]):
::: incremental
- If people don’t know why your project exists, they won’t use it.
- If people can’t figure out how to install your code, they won’t use it.
- If people can’t figure out how to use your code, they won’t use it.
:::
:::
::: {.column width="50%"}
:::
:::
## FA<span style="color:red">IR</span>4RS: Document your code!{.smaller}
<br>
::: {.columns}
::: {.column width="50%"}
A little poem from [A beginner’s guide to writing documentation](https://www.writethedocs.org/guide/writing/beginners-guide-to-docs/]):
- If people don’t know why your project exists, they won’t use it.
- If people can’t figure out how to install your code, they won’t use it.
- If people can’t figure out how to use your code, they won’t use it.
In practice, Github can host documentation as website (and it is very easy to do!) :arrow_right::arrow_right:
:::
::: {.column width="50%"}
{.absolute top="100" left="550" width="500" height="350"}
{.absolute top="350" left="650" width="400" height="250"}
:::
:::
## FA<span style="color:red">IR</span>4RS: Licence your code!{.smaller}
::: {.columns}
::: {.column width="50%"}
You need to tell people how they can re-use your code.
::: incremental
- GPLv3 [The GNU General Public License](https://www.gnu.org/licenses/gpl-3.0.en.html): a free, copyleft license for software and other kinds of works. It is intended to guarantee your freedom to share and change all versions of a software to make sure it remains free software for all its users
- [MIT licence](https://opensource.org/license/mit/): is a permissive free software license. Without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
:::
:::
::: {.column width="50%"}
{.absolute top="100" left="550" width="500" height="280"}
<br><br><br><br><br><br><br><br><br><br>
<span style="color:red">The licence must be made clear in the code repository and in the documentation.</span>
:::
:::
## FA<span style="color:red">IR</span>4RS: Get credit for your work{.smaller}
If people are using your software you should get credit for it.
:arrow_right: state how you want to be credited. You can add it in the documentation and/or create a [citation.cff](https://citation-file-format.github.io/) file that you can add with your code ([tools](https://citation-file-format.github.io/cff-initializer-javascript/#/). are available to generate them)
{.absolute top="250" left="550" width="500" height="280"}
{.absolute top="290" left="20" width="500" height="200"}
## FA<span style="color:red">IR</span>4RS: Share it!{.smaller}
::: {.columns}
::: {.column width="50%"}
- Create a description of your code with metadata [data about your software].
- Codemeta is a set of keywords used to describe code and how to structure them in a machine readable way<br>
Examples:
::: incremental
- The citation.cff file contains metadata
- Description keywords
- Url to repository, to documentation
- List of contributors and affiliations
- etc…
:::
:::
::: {.column width="50%"}
{.absolute top="150" left="650" width="400" height="300"}
:::
:::
## FA<span style="color:red">IR</span>4RS: Share it!{.smaller}
::: {.columns}
::: {.column width="50%"}
<br>
In order to ensure that others can access and download your code, and that this access remains permanent over time, you should deposit your code in a repository. Two types:
- General purpose
- Domain Specific
<span style="color:red"> Choose what makes more sense for you project! </span>
:::
::: {.column width="50%"}
{.absolute top="200" left="550" width="500" height="300"}
:::
:::
## FA<span style="color:red">IR</span>4RS: Share it!{.smaller}
::: {.columns}
::: {.column width="50%"}
<br>
In order to ensure that others can access and download your code, and that this access remains permanent over time, you should deposit your code in a repository. Two types:
- General purpose
- Domain Specific
<span style="color:red">Choose what makes more sense for you project!</span>
:::
::: {.column width="50%"}
{.absolute top="80" left="600" width="400" height="200"}<br><br><br><br><br><br>
<span style="color:red">Numerous repositories give your content a DOI [Digital Object Identifier]</span>
It means it can be cited in publication and other communications in order to open up your research to others and invite collaboration, as well as ensuring a constant link to your code.
:::
:::
## <span style="color:red">FA</span>IR4RS: Publish it!{.smaller}
<br>
::: {.columns}
::: {.column width="50%"}
- Generalist software journals
- [JOSS](https://joss.theoj.org/): Journal of Open Source Software:
<font size=3>Academic journal with a formal peer review process that is designed to improve the quality of the software submitted. </font>
- [JORS](https://openresearchsoftware.metajnl.com/): Journal of Open Research Software:
<font size=3> Features peer reviewed Software Metapapers describing research software with high reuse potential. </font>
- [Software Impacts](https://www.sciencedirect.com/journal/software-impacts):
<font size=3>multidisciplinary, open access, peer-reviewed journal which publishes short, articles that describe software which addresses a research challenge. </font>
:::
::: {.column width="50%"}
- Some are domain specific:
- Astronomy and computing
- Journal of Artificial Societies and Social Simulation
- Journal of Statistical Software
- Science of Computer Programming
- Computer Methods and Programs in Biomedicine
:::
:::
You can find a list of potential journals [here](https://www.software.ac.uk/top-tip/which-journals-should-i-publish-my-software)
# The FAIR<sup>2</sup>4RS training programme at the University
## Lack of skills for developing software
::: {.columns}
::: {.column width="50%"}
<br><br>
Do you feel that you have received sufficient training to develop reliable software?
<font size=3>Bob Turner & Paul Richmond, UoS, RSE team, [github.com/RSE-Sheffield/sssurvey](rse.shef.ac.uk/sssurvey). </font>
:::
::: {.column width="50%"}
{.absolute top="200" left="550" width="500" height="200"}
:::
:::
## The FAIR<sup>2</sup>4RS Programme: Overview
{fig-align="center"}
## Software Lifecycle Planning
::: {.columns}
::: {.column width="50%"}
<br>
<span style="color:red">Who</span>:
[R Thomas](mailto:[email protected]), [R. Campbell](), [K. O’Neill]()
<span style="color:red">When/Length</span>: November 8th / 2.5h (afternoon)
<span style="color:red">Format</span>: Online
:::
::: {.column width="50%"}
<font size=5>
<ins>Abstract:</ins>
When you start writing software it is often very useful to think about the development process and how you will make your software sustainable in the long term. In this module we will introduce important aspects of software development in research: <span style="color:red">*software management plan, licences and dissemination*</span>. This module should allow you to ask yourself the right questions when starting a research software project.
</font>
:::
:::
## Version control: Git, GitHub and GitKraken - From Zero to Hero
::: {.columns}
::: {.column width="50%"}
<br>
<span style="color:red">Who</span>: [Neil Shephard](mailto:[email protected])
<span style="color:red">When/Length</span>: 18/19 November (2 half days). Another session in February
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<ins>Abstract:</ins>
If you’ve never heard of or used version control and Git before this is the course for you. We start by introducing version control and exploring how it can be beneficial to researchers, then we introduce some useful tools and get started with some basic workflow using these tools. We build on those foundations with collaborative exercises that introduce key concepts such as forks, pull requests and branches and give you the chance to <span style="color:red">*get some hands-on experience with using version control in a research setting*</span>.
</font>
:::
:::
## [Advanced] Version control: Git collaboration
::: {.columns}
::: {.column width="50%"}
<br>
<span style="color:red">Who</span>: [Neil Shephard](mailto:[email protected])
<span style="color:red">When/Length</span>: February
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<ins>Abstract:</ins>
This course aims to help you develop a <span style="color:red">*deeper understanding of how Git works to facilitate collaboration*</span>. It builds on foundations laid by the Git beginners course. The core idea around the course is that by improving your understanding of working with branches and how to make your commits tidier and neater it makes it easier to understand pull requests and Git history which in turn makes it easier to collaborate and work on code with others (including your future self!).
</font>
:::
:::
## Design your code (and write less of it)
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [R. Thomas](mailto:[email protected])
<span style="color:red">When/Length</span>: 12/13 December (2 half days)
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<ins>Abstract:</ins>
The way you write your code will have a massive impact on how easy it is to maintain in the long run. <span style="color:red">*This course on Code Design introduces essential principles and best practices for writing clean and maintainable code*</span>. We will learn how we can write clean code, adhering to naming conventions, commenting, and following PEP 8 guidelines. We will then explore some fundamental principles such as DRY, KISS or YAGNI that are important to keep in mind when writing new code and see how we can spend less time touching the code by introducing configuration files and command line interface.
</font>
:::
:::
## Code Testing
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [Sylvia Whittle](mailto:[email protected])
<span style="color:red">When/Length</span>: January (half day)
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<ins>Abstract:</ins>
Does your code work? Are you sure? How do you ensure that it keeps working when you change it? Manually verifying is slow and tedious. Why not automate it? Software testing checks that your code works for you, and when it breaks, it can show you exactly where it broke, without you having to trawl through hundreds of lines of code manually.<span style="color:red">*This course aims to provide you with the tools you need to start automatically ensuring the reliability of your code.*</span>
</font>
:::
:::
## Documentation
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [Joe Heffer](mailto:[email protected])
<span style="color:red">When/Length</span>: February (half day)
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<br>
<ins>Abstract:</ins>
Well-documented software promotes reproducibility, maintainability, and increased research impact through wider adoption and citation. <span style="color:red">*This course teaches researchers how to document their software effectively, making it accessible and understandable to others.*</span> It covers topics such as writing readable code and usage instructions.
</font>
:::
:::
## Reproducible Environments
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [Dan Brady](mailto:[email protected])
<span style="color:red">When/Length</span>: March [half day]
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<br>
<ins>Abstract:</ins>
Ensuring that others are able to take your code, run it, and are able to produce the same (or equivalent) results is one of the key tenets of FAIR and reproducible research software. <span style="color:red">*This course will provide you with an overview of different ways to make your code reproducible*</span> and then focus on virtual environments as a specific tool for computational reproducibility.
</font>
:::
:::
## Packaging
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [Chris Wild]() and [Farhad Allian]()
<span style="color:red">When/Length</span>: April [half day]
<span style="color:red">Format</span>: In person
:::
::: {.column width="50%"}
<font size=5>
<br>
<ins>Abstract:</ins>
Packaging your software is one of the most important steps in a software project to make it both findable and accessible. <span style="color:red">*This course will provide you with an understanding of why and when packaging is useful*</span>, what different standards exist to package Python projects and take you through each step of the packaging process.
</font>
:::
:::
## Software Papers
::: {.columns}
::: {.column width="50%"}
<br><br>
<span style="color:red">Who</span>: [Romain Thomas](mailto:[email protected]) & [Arfon Smith]()
<span style="color:red">When/Length</span>: April, 1.5h