From ec9c5b01a8ff4c91a86d2fe32e1df6b11d59a9d4 Mon Sep 17 00:00:00 2001
From: Romain
Date: Thu, 3 Sep 2020 10:17:35 -0400
Subject: [PATCH 1/4] add jupyter to requirements-dev to export doc
---
requirements-dev.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 156f21a..169a600 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -10,3 +10,4 @@ mkdocstrings
pytest
pytest-cov
requests
+jupyter
From d25de6ec7fc16632ed7e1ae8a226258a5ee86ae0 Mon Sep 17 00:00:00 2001
From: Romain
Date: Thu, 3 Sep 2020 10:18:04 -0400
Subject: [PATCH 2/4] Add JOSS paper link and "Citing Pyomeca" section
---
README.md | 49 ++++++++++++++++++++++++++++++++++++++-----------
docs/about.md | 32 ++++++++++++++------------------
2 files changed, 52 insertions(+), 29 deletions(-)
diff --git a/README.md b/README.md
index fa89b13..5b89d8a 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,11 @@
src="https://raw.githubusercontent.com/pyomeca/design/master/logo/logo_plain_doc.svg?sanitize=true"
alt="logo"
/>
+
-
-
Pyomeca is a python library allowing you to carry out a complete biomechanical analysis; in a simple, logical and concise way.
@@ -141,7 +136,39 @@ Pyomeca is Apache-licensed and the source code is available on [GitHub](https://
If any questions or issues come up as you use pyomeca, please get in touch via [GitHub issues](https://github.com/pyomeca/pyomeca/issues).
We welcome any input, feedback, bug reports, and contributions.
-## Contributors and support
+## Citing Pyomeca
+
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02431/status.svg)](https://doi.org/10.21105/joss.02431)
+
+If you use pyomeca in your academic work, please consider citing [our paper](https://doi.org/10.21105/joss.02431) as:
+
+```bibtex
+@article{Martinez2020,
+ doi = {10.21105/joss.02431},
+ url = {https://doi.org/10.21105/joss.02431},
+ year = {2020},
+ publisher = {The Open Journal},
+ volume = {5},
+ number = {53},
+ pages = {2431},
+ author = {Romain Martinez and Benjamin Michaud and Mickael Begon},
+ title = {`pyomeca`: An Open-Source Framework for Biomechanical Analysis},
+ journal = {Journal of Open Source Software}
+}
+```
+
+Please consider citing the [xarray](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.148/) project, which pyomeca is based on:
+
+```bibtex
+@article{jors-xarray,
+title = {Xarray: N-D labeled arrays and datasets in Python},
+author = {Joe Hamman and Stephan Hoyer},
+year = {2017},
+journal = {Journal of Open Research Software}
+}
+```
+
+## Contributors
- [Romain Martinez](https://github.com/romainmartinez)
- [Benjamin Michaud](https://github.com/pariterre)
diff --git a/docs/about.md b/docs/about.md
index 95ace44..18a9c57 100644
--- a/docs/about.md
+++ b/docs/about.md
@@ -4,29 +4,23 @@ Pyomeca is Apache-licensed and the source code is available on [GitHub](https://
## Citing Pyomeca
-If you use pyomeca in your academic work, please consider citing [our paper](https://github.com/openjournals/joss-papers/blob/joss.02323/joss.02323/10.21105.joss.02323.pdf) as:
+If you use pyomeca in your academic work, please consider citing [our paper](https://doi.org/10.21105/joss.02431) as:
```bibtex
-@unpublished{Martinez2020,
- doi = {},
- url = {},
+@article{Martinez2020,
+ doi = {10.21105/joss.02431},
+ url = {https://doi.org/10.21105/joss.02431},
year = {2020},
publisher = {The Open Journal},
- volume = {},
- number = {},
- pages = {},
+ volume = {5},
+ number = {53},
+ pages = {2431},
author = {Romain Martinez and Benjamin Michaud and Mickael Begon},
- title = {Pyomeca: An Open-Source Framework for Biomechanical Analysis},
+ title = {`pyomeca`: An Open-Source Framework for Biomechanical Analysis},
journal = {Journal of Open Source Software}
}
```
-!!! note
-
- Our paper is currently under review.
- You can follow the review process [here](https://github.com/openjournals/joss-reviews/issues/2323).
- Once available, we will update the BibTex entry.
-
Please consider citing the [xarray](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.148/) project, which pyomeca is based on:
```bibtex
@@ -40,15 +34,17 @@ journal = {Journal of Open Research Software}
## Papers using Pyomeca
-- Blache, Yoann, Romain Martinez, Raphaël Dumas, Mickael Begon, Nicola Hagemeister, and Sonia Duprey. 2019. “[Chapter 20 - Motion Analysis and Modeling of the Shoulder: Challenges and Potential Applications.](https://www.sciencedirect.com/science/article/pii/B9780128167137000209)” In DHM and Posturography, edited by Sofia Scataglini and Gunther Paul, 261–271. Academic Press. doi:10.1016/B978-0-12-816713-7.00020-9.
+- Martinez Romain, Benjamin Michaud, Mickael Begon. 2020. “[`pyomeca`: An Open-Source Framework for Biomechanical Analysis](https://doi.org/10.21105/joss.02431)” Journal of Open Source Software.
-- Bouffard, Jason, Romain Martinez, André Plamondon, Julie N. Côté, and Mickaël Begon. 2019. “[Sex Differences in Glenohumeral Muscle Activation and Coactivation during a Box Lifting Task.](https://doi.org/10.1080/00140139.2019.1640396)” Ergonomics 62 (10). Taylor & Francis: 1327–1338. doi:10.1080/00140139.2019.1640396.
+- Assila Najoua, Claudio Pizzolato, Romain Martinez, David Lloyd, Mickael Begon. 2020. “[EMG-Assisted Algorithm to Account for Shoulder Muscles Co-Contraction in Overhead Manual Handling.](https://doi.org/10.3390/app10103522)” Applied Sciences.
- Martinez, Romain, Najoua Assila, Etienne Goubault, and Mickaël Begon. 2020. “[Sex Differences in Upper Limb Musculoskeletal Biomechanics during a Lifting Task.](https://doi.org/10.1016/j.apergo.2020.103106)” Applied Ergonomics 86 (July): 103106. doi:10.1016/j.apergo.2020.103106.
-- Martinez, Romain, Jason Bouffard, Benjamin Michaud, André Plamondon, Julie N. Côté, and Mickaël Begon. 2019. “[Sex Differences in Upper Limb 3D Joint Contributions during a Lifting Task.](https://doi.org/10.1080/00140139.2019.1571245)” Ergonomics 62 (5): 682–693. doi:10.1080/00140139.2019.1571245.
+- Blache, Yoann, Romain Martinez, Raphaël Dumas, Mickael Begon, Nicola Hagemeister, and Sonia Duprey. 2019. “[Chapter 20 - Motion Analysis and Modeling of the Shoulder: Challenges and Potential Applications.](https://www.sciencedirect.com/science/article/pii/B9780128167137000209)” In DHM and Posturography, edited by Sofia Scataglini and Gunther Paul, 261–271. Academic Press. doi:10.1016/B978-0-12-816713-7.00020-9.
-- Assila Najoua, Claudio Pizzolato, Romain Martinez, David Lloyd, Mickael Begon. 2020. “[EMG-Assisted Algorithm to Account for Shoulder Muscles Co-Contraction in Overhead Manual Handling.](https://doi.org/10.3390/app10103522)” Applied Sciences.
+- Bouffard, Jason, Romain Martinez, André Plamondon, Julie N. Côté, and Mickaël Begon. 2019. “[Sex Differences in Glenohumeral Muscle Activation and Coactivation during a Box Lifting Task.](https://doi.org/10.1080/00140139.2019.1640396)” Ergonomics 62 (10). Taylor & Francis: 1327–1338. doi:10.1080/00140139.2019.1640396.
+
+- Martinez, Romain, Jason Bouffard, Benjamin Michaud, André Plamondon, Julie N. Côté, and Mickaël Begon. 2019. “[Sex Differences in Upper Limb 3D Joint Contributions during a Lifting Task.](https://doi.org/10.1080/00140139.2019.1571245)” Ergonomics 62 (5): 682–693. doi:10.1080/00140139.2019.1571245.
## Contributors and support
From 62de9fa24674820f01fa93ba15df0911a2bfe144 Mon Sep 17 00:00:00 2001
From: Romain
Date: Thu, 3 Sep 2020 10:42:17 -0400
Subject: [PATCH 3/4] add paper that used pyomeca
---
docs/about.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/docs/about.md b/docs/about.md
index 18a9c57..5a1f0dd 100644
--- a/docs/about.md
+++ b/docs/about.md
@@ -34,6 +34,8 @@ journal = {Journal of Open Research Software}
## Papers using Pyomeca
+- Grontman Anita, Łukasz Horyza, Krzystof Koczan, Małgorzata Marzec, Maciej Śmiertka, Maciej Trybał. 2020. "[Analysis of sword fencing training evaluation possibilities using Motion Capture techniques](https://doi.org/10.1109/SoSE50414.2020.9130469)." IEEE 15th International Conference of System of Systems Engineering.
+
- Martinez Romain, Benjamin Michaud, Mickael Begon. 2020. “[`pyomeca`: An Open-Source Framework for Biomechanical Analysis](https://doi.org/10.21105/joss.02431)” Journal of Open Source Software.
- Assila Najoua, Claudio Pizzolato, Romain Martinez, David Lloyd, Mickael Begon. 2020. “[EMG-Assisted Algorithm to Account for Shoulder Muscles Co-Contraction in Overhead Manual Handling.](https://doi.org/10.3390/app10103522)” Applied Sciences.
From 058bd34377f08fcb8e92666050ed490149f776d4 Mon Sep 17 00:00:00 2001
From: Romain
Date: Thu, 3 Sep 2020 10:47:06 -0400
Subject: [PATCH 4/4] add paper that used pyomeca
---
docs/about.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/docs/about.md b/docs/about.md
index 5a1f0dd..93d5983 100644
--- a/docs/about.md
+++ b/docs/about.md
@@ -34,6 +34,8 @@ journal = {Journal of Open Research Software}
## Papers using Pyomeca
+- Konrad Kluwak, Niżyński Teodor. 2020. "[Gait Classification using LSTM Networks for Tagging System](https://doi.org/10.1109/SoSE50414.2020.9130487)." IEEE 15th International Conference of System of Systems Engineering.
+
- Grontman Anita, Łukasz Horyza, Krzystof Koczan, Małgorzata Marzec, Maciej Śmiertka, Maciej Trybał. 2020. "[Analysis of sword fencing training evaluation possibilities using Motion Capture techniques](https://doi.org/10.1109/SoSE50414.2020.9130469)." IEEE 15th International Conference of System of Systems Engineering.
- Martinez Romain, Benjamin Michaud, Mickael Begon. 2020. “[`pyomeca`: An Open-Source Framework for Biomechanical Analysis](https://doi.org/10.21105/joss.02431)” Journal of Open Source Software.