From 57797ab043f8fa8b8e82b5df5a18d66b85e235f8 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 11 Apr 2022 13:58:31 -0400 Subject: [PATCH 01/49] initial commit of paper.md (with example or placeholder text) --- doc/source/tracking/paper.md | 103 +++++++++++++++++++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 doc/source/tracking/paper.md diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md new file mode 100644 index 000000000..3323155c8 --- /dev/null +++ b/doc/source/tracking/paper.md @@ -0,0 +1,103 @@ +--- +title: 'icepyx' +tags: + - Python + - ICESat-2 + - data access + - LiDAR + - elevation + - community +authors: + - name: Jessica Scheick^[Co-first author] # note this makes a footnote saying 'Co-first author' + orcid: 0000-0000-0000-0000 + affiliation: "1, 2" # (Multiple affiliations must be quoted) + - name: Author Without ORCID^[Co-first author] # note this makes a footnote saying 'Co-first author' + affiliation: 2 + - name: Author with no affiliation^[Corresponding author] + affiliation: 3 +affiliations: + - name: University of New Hampshire, USA + index: 1 + - name: Institution Name, Country + index: 2 + - name: Independent Researcher, Country + index: 3 +date: 18 April 2022 +bibliography: icepyx_pubs.bib + +# Optional fields if submitting to a AAS journal too, see this blog post: +# https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing +aas-doi: +aas-journal: +--- + +# Summary + +icepyx is both a software library and a community composed of ICESat-2 data users, developers, and the scientific community. +We are working together to develop a shared library of resources - including existing resources, new code, tutorials, and use-cases/examples - that simplify the process of querying, obtaining, analyzing, and manipulating ICESat-2 datasets to enable scientific discovery. + +# Statement of need + +icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science, and reproducible workflows by integrating and sharing resources. + +Many of the underlying tools from which icepyx was developed began as Jupyter Notebooks developed for and during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019 or as scripts written and used by the ICESat-2 Science Team members. This project combines and generalizes these scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. It also improves interoperability for ICESat-2 datasets with other open-source tools. Our resources guide provides additional information on both the foundational documents for icepyx and closely related libraries for working with ICESat-2 data. + +(Example text) +`Gala` was designed to be used by both astronomical researchers and by +students in courses on gravitational dynamics or astronomy. It has already been +used in a number of scientific publications [@Pearson:2017] and has also been +used in graduate courses on Galactic dynamics to, e.g., provide interactive +visualizations of textbook material [@Binney:2008]. The combination of speed, +design, and support for Astropy functionality in `Gala` will enable exciting +scientific explorations of forthcoming data releases from the *Gaia* mission +[@gaia] by students and experts alike. + +# Mathematics + +Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$ + +Double dollars make self-standing equations: + +$$\Theta(x) = \left\{\begin{array}{l} +0\textrm{ if } x < 0\cr +1\textrm{ else} +\end{array}\right.$$ + +You can also use plain \LaTeX for equations +\begin{equation}\label{eq:fourier} +\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx +\end{equation} +and refer to \autoref{eq:fourier} from text. + +# Citations + +Citations to entries in paper.bib should be in +[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) +format. + +If you want to cite a software repository URL (e.g. something on GitHub without a preferred +citation) then you can do it with the example BibTeX entry below for @fidgit. + +For a quick reference, the following citation commands can be used: +- `@author:2001` -> "Author et al. (2001)" +- `[@author:2001]` -> "(Author et al., 2001)" +- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" + +# Figures + +Figures can be included like this: +![Caption for example figure.\label{fig:example}](figure.png) +and referenced from text using \autoref{fig:example}. + +Figure sizes can be customized by adding an optional second parameter: +![Caption for example figure.](figure.png){ width=20% } + +Figures to include: icepyx in context of other tools + +# Acknowledgements + +We acknowledge funding support from NASA and the University of Washington eScience Institute. +Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance +in establishing this library and welcoming us to the open-source community. + +# References \ No newline at end of file From dac12fe6cae9ab8f3916fb5e19ce2da061732cb8 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 5 May 2022 12:38:14 -0400 Subject: [PATCH 02/49] populate author and acknowledge list from github commits --- doc/source/tracking/paper.md | 64 +++++++++++++++++++++++++++++++++--- 1 file changed, 59 insertions(+), 5 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 3323155c8..2557623ce 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -8,13 +8,53 @@ tags: - elevation - community authors: - - name: Jessica Scheick^[Co-first author] # note this makes a footnote saying 'Co-first author' + - name: Jessica Scheick^[Corresponding author] # note this makes a footnote orcid: 0000-0000-0000-0000 affiliation: "1, 2" # (Multiple affiliations must be quoted) - - name: Author Without ORCID^[Co-first author] # note this makes a footnote saying 'Co-first author' + - name: Wei Ji Leong affiliation: 2 - - name: Author with no affiliation^[Corresponding author] + - name: Kelsey Bisson affiliation: 3 + - name: + affiliation: 3 + - name: + affiliation: 3 + - name: + affiliation: 3 + - name: + affiliation: 3 + - name: + affiliation: 3 + +Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes to reviewing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. + +Jessica Scheick +Wei Ji Leong +Kelsey Bisson + +Anthony Arendt +Shashank B +Zach Fair +Raphael Hagen +Scott Henderson +Friedrich Knuth +Tian Li +Zheng Liu +Romina Piunno +Facu Sapienza +Landung "Don" Setiawan +Trey Stafford +Amy Steiker +Tyler Sutterley +Bruce Wallin +Learn2Pheonix + + + + + + + affiliations: - name: University of New Hampshire, USA index: 1 @@ -97,7 +137,21 @@ Figures to include: icepyx in context of other tools # Acknowledgements We acknowledge funding support from NASA and the University of Washington eScience Institute. -Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance -in establishing this library and welcoming us to the open-source community. +Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance in establishing this library and welcoming us to the open-source community. +Amy Steiker, Mikala Beig, Nick Kotlinski, Luis Lopez, and many others at the National Snow and Ice Data Center (NSIDC) provide technical support and data access guidance. +The icepyx contributors list also includes many Hackweek planners and participants who shared ideas and embraced the opportunity to engage in open-science practices. + + + # References \ No newline at end of file From b44aaf89cc61e20e83c0624097511eda21611299 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 29 Aug 2022 10:10:07 -0400 Subject: [PATCH 03/49] add author list and update descriptions --- doc/source/tracking/paper.md | 160 ++++++++++++++++++----------------- 1 file changed, 81 insertions(+), 79 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 2557623ce..53981e4ba 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -3,10 +3,10 @@ title: 'icepyx' tags: - Python - ICESat-2 - - data access - LiDAR - elevation - community + - cloud authors: - name: Jessica Scheick^[Corresponding author] # note this makes a footnote orcid: 0000-0000-0000-0000 @@ -15,54 +15,77 @@ authors: affiliation: 2 - name: Kelsey Bisson affiliation: 3 - - name: - affiliation: 3 - - name: - affiliation: 3 - - name: - affiliation: 3 - - name: - affiliation: 3 - - name: - affiliation: 3 - -Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes to reviewing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. - -Jessica Scheick -Wei Ji Leong -Kelsey Bisson - -Anthony Arendt -Shashank B -Zach Fair -Raphael Hagen -Scott Henderson -Friedrich Knuth -Tian Li -Zheng Liu -Romina Piunno -Facu Sapienza -Landung "Don" Setiawan -Trey Stafford -Amy Steiker -Tyler Sutterley -Bruce Wallin -Learn2Pheonix - - - - - - + - name: Anthony Arendt + affiliation: 4 + - name: Shashank Bhushan + affiliation: 4 + - name: Zach Fair + affiliation: 5 + - name: Raphael Hagen + affiliation: 4 + - name: Sarah Hall + affiliation: 1 + - name: Scott Henderson + affiliation: 4 + - name: Tom Johnson + affiliation: 6 + - name: Friedrich Knuth + affiliation: 7 + - name: Tian Li + affiliation: 8 + - name: Zheng Liu + affiliation: 4 + - name: Luis Lopez + affiliation: 9 + - name: Romina Piunno + affiliation: 10 + - name: Nitin Ravinder + affiliation: 11 + - name: Landung "Don" Setiawan + affiliation: 4 + - name: Trey Stafford + affiliation: 9 + - name: Amy Steiker + affiliation: 9 + - name: Tyler Sutterley + affiliation: 4 + - name: JP Swinski + affiliation: 12 + - name: Bruce Wallin + affiliation: 9 + - name: Learn2Pheonix + affiliation: 13 + +# Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes to preparing (including reviewing) the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. affiliations: - name: University of New Hampshire, USA index: 1 - - name: Institution Name, Country + - name: Ohio State University, USA index: 2 - - name: Independent Researcher, Country + - name: University of Colorado Boulder, USA index: 3 -date: 18 April 2022 + - name: , USA + index: 4 + - name: , USA + index: 5 + - name: , USA + index: 6 + - name: , USA + index: 7 + - name: , USA + index: 8 + - name: , USA + index: 9 + - name: , USA + index: 10 + - name: , USA + index: 11 + - name: , USA + index: 12 + - name: , USA + index: 13 +date: 1 September 2022 bibliography: icepyx_pubs.bib # Optional fields if submitting to a AAS journal too, see this blog post: @@ -73,41 +96,14 @@ aas-journal: # Summary -icepyx is both a software library and a community composed of ICESat-2 data users, developers, and the scientific community. +icepyx is both a software library and a community composed of ICESat-2 data users, developers, maintainers, and the scientific community. We are working together to develop a shared library of resources - including existing resources, new code, tutorials, and use-cases/examples - that simplify the process of querying, obtaining, analyzing, and manipulating ICESat-2 datasets to enable scientific discovery. # Statement of need -icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science, and reproducible workflows by integrating and sharing resources. - -Many of the underlying tools from which icepyx was developed began as Jupyter Notebooks developed for and during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019 or as scripts written and used by the ICESat-2 Science Team members. This project combines and generalizes these scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. It also improves interoperability for ICESat-2 datasets with other open-source tools. Our resources guide provides additional information on both the foundational documents for icepyx and closely related libraries for working with ICESat-2 data. - -(Example text) -`Gala` was designed to be used by both astronomical researchers and by -students in courses on gravitational dynamics or astronomy. It has already been -used in a number of scientific publications [@Pearson:2017] and has also been -used in graduate courses on Galactic dynamics to, e.g., provide interactive -visualizations of textbook material [@Binney:2008]. The combination of speed, -design, and support for Astropy functionality in `Gala` will enable exciting -scientific explorations of forthcoming data releases from the *Gaia* mission -[@gaia] by students and experts alike. +icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science practices, and reproducible workflows by integrating and sharing resources. -# Mathematics - -Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$ - -Double dollars make self-standing equations: - -$$\Theta(x) = \left\{\begin{array}{l} -0\textrm{ if } x < 0\cr -1\textrm{ else} -\end{array}\right.$$ - -You can also use plain \LaTeX for equations -\begin{equation}\label{eq:fourier} -\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx -\end{equation} -and refer to \autoref{eq:fourier} from text. +icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@Bisson:2021; @li:2020] and Hackweeks [@Scheick:2022]. # Citations @@ -132,25 +128,31 @@ and referenced from text using \autoref{fig:example}. Figure sizes can be customized by adding an optional second parameter: ![Caption for example figure.](figure.png){ width=20% } -Figures to include: icepyx in context of other tools +Figures to include: icepyx in context of other tools? # Acknowledgements We acknowledge funding support from NASA and the University of Washington eScience Institute. Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance in establishing this library and welcoming us to the open-source community. Amy Steiker, Mikala Beig, Nick Kotlinski, Luis Lopez, and many others at the National Snow and Ice Data Center (NSIDC) provide technical support and data access guidance. -The icepyx contributors list also includes many Hackweek planners and participants who shared ideas and embraced the opportunity to engage in open-science practices. +The icepyx contributors list also includes many wonderful folks who shared ideas, provided mentoring, and embraced the opportunity to engage in open-science practices while working with ICESat-2 data products. - From 1b2e9935e6d88646c3f215c0939c78a6dfbdc7b6 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 29 Aug 2022 10:14:28 -0400 Subject: [PATCH 04/49] add temp action for testing pdf compiling --- .github/workflows/draft-pdf.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .github/workflows/draft-pdf.yml diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml new file mode 100644 index 000000000..c67efb6c3 --- /dev/null +++ b/.github/workflows/draft-pdf.yml @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v2 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: doc/source/tracking/paper.md + - name: Upload + uses: actions/upload-artifact@v1 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper.pdf \ No newline at end of file From bbe32f8052fcdc612a9683d79fc83140bf8f5b40 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 29 Aug 2022 10:16:58 -0400 Subject: [PATCH 05/49] add unsaved changes --- doc/source/tracking/paper.md | 87 +++++++++++++----------------------- 1 file changed, 31 insertions(+), 56 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 53981e4ba..688d92bc9 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -10,7 +10,7 @@ tags: authors: - name: Jessica Scheick^[Corresponding author] # note this makes a footnote orcid: 0000-0000-0000-0000 - affiliation: "1, 2" # (Multiple affiliations must be quoted) + affiliation: 1 - name: Wei Ji Leong affiliation: 2 - name: Kelsey Bisson @@ -26,35 +26,35 @@ authors: - name: Sarah Hall affiliation: 1 - name: Scott Henderson - affiliation: 4 - - name: Tom Johnson - affiliation: 6 - - name: Friedrich Knuth - affiliation: 7 - - name: Tian Li - affiliation: 8 - - name: Zheng Liu - affiliation: 4 - - name: Luis Lopez - affiliation: 9 - - name: Romina Piunno - affiliation: 10 - - name: Nitin Ravinder - affiliation: 11 - - name: Landung "Don" Setiawan - affiliation: 4 - - name: Trey Stafford - affiliation: 9 - - name: Amy Steiker - affiliation: 9 - - name: Tyler Sutterley - affiliation: 4 - - name: JP Swinski - affiliation: 12 - - name: Bruce Wallin - affiliation: 9 - - name: Learn2Pheonix - affiliation: 13 + affiliation: 4 + - name: Tom Johnson + affiliation: 6 + - name: Friedrich Knuth + affiliation: 7 + - name: Tian Li + affiliation: 8 + - name: Zheng Liu + affiliation: 4 + - name: Luis Lopez + affiliation: 9 + - name: Romina Piunno + affiliation: 10 + - name: Nitin Ravinder + affiliation: 11 + - name: Landung "Don" Setiawan + affiliation: 4 + - name: Trey Stafford + affiliation: 9 + - name: Amy Steiker + affiliation: 9 + - name: Tyler Sutterley + affiliation: 4 + - name: JP Swinski + affiliation: 12 + - name: Bruce Wallin + affiliation: 9 + - name: Learn2Pheonix + affiliation: 13 # Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes to preparing (including reviewing) the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. @@ -103,32 +103,7 @@ We are working together to develop a shared library of resources - including exi icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science practices, and reproducible workflows by integrating and sharing resources. -icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@Bisson:2021; @li:2020] and Hackweeks [@Scheick:2022]. - -# Citations - -Citations to entries in paper.bib should be in -[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) -format. - -If you want to cite a software repository URL (e.g. something on GitHub without a preferred -citation) then you can do it with the example BibTeX entry below for @fidgit. - -For a quick reference, the following citation commands can be used: -- `@author:2001` -> "Author et al. (2001)" -- `[@author:2001]` -> "(Author et al., 2001)" -- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" - -# Figures - -Figures can be included like this: -![Caption for example figure.\label{fig:example}](figure.png) -and referenced from text using \autoref{fig:example}. - -Figure sizes can be customized by adding an optional second parameter: -![Caption for example figure.](figure.png){ width=20% } - -Figures to include: icepyx in context of other tools? +icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@https://doi.org/10.1029/2021GL095051; @tc-14-3629-2020] and Hackweeks [@Scheick:2022]. # Acknowledgements From af41e2450182981a3794d98c3823f99dbd6452bb Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 30 Aug 2022 11:31:14 -0400 Subject: [PATCH 06/49] add IDs and affiliations Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> Co-authored-by: Tyler Sutterley --- doc/source/tracking/paper.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 688d92bc9..d9aab1286 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -12,6 +12,7 @@ authors: orcid: 0000-0000-0000-0000 affiliation: 1 - name: Wei Ji Leong + orcid: 0000-0003-2354-1988 affiliation: 2 - name: Kelsey Bisson affiliation: 3 @@ -48,6 +49,7 @@ authors: - name: Amy Steiker affiliation: 9 - name: Tyler Sutterley + orcid: 0000-0002-6964-1194 affiliation: 4 - name: JP Swinski affiliation: 12 @@ -61,13 +63,13 @@ authors: affiliations: - name: University of New Hampshire, USA index: 1 - - name: Ohio State University, USA + - name: The Ohio State University, USA index: 2 - name: University of Colorado Boulder, USA index: 3 - name: , USA index: 4 - - name: , USA + - name: University of Washington, USA index: 5 - name: , USA index: 6 From 360deff925db5466a209b4ae0ac0b366cbcea1ee Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 30 Aug 2022 11:36:23 -0400 Subject: [PATCH 07/49] add id --- doc/source/tracking/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index d9aab1286..df508be8f 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -9,7 +9,7 @@ tags: - cloud authors: - name: Jessica Scheick^[Corresponding author] # note this makes a footnote - orcid: 0000-0000-0000-0000 + orcid: 0000-0002-3421-4459 affiliation: 1 - name: Wei Ji Leong orcid: 0000-0003-2354-1988 @@ -58,7 +58,7 @@ authors: - name: Learn2Pheonix affiliation: 13 -# Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes to preparing (including reviewing) the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. +# Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. affiliations: - name: University of New Hampshire, USA From 39cb6e208790e989aee123af124e3d7f6bdcb328 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 30 Aug 2022 11:39:10 -0400 Subject: [PATCH 08/49] add rest of refs to text --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index df508be8f..609152e02 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -105,7 +105,7 @@ We are working together to develop a shared library of resources - including exi icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science practices, and reproducible workflows by integrating and sharing resources. -icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@https://doi.org/10.1029/2021GL095051; @tc-14-3629-2020] and Hackweeks [@Scheick:2022]. +icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. # Acknowledgements From eb58e469a456b823357688774ef249680ca1218f Mon Sep 17 00:00:00 2001 From: Romina Piunno Date: Tue, 30 Aug 2022 13:17:47 -0400 Subject: [PATCH 09/49] added affiliation for Romina --- doc/source/tracking/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 609152e02..a6959f66d 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -79,7 +79,7 @@ affiliations: index: 8 - name: , USA index: 9 - - name: , USA + - name: University of Toronto, Canada index: 10 - name: , USA index: 11 @@ -133,4 +133,4 @@ Molly Wieringa Bidhya --> -# References \ No newline at end of file +# References From b4fe4401d6b5358db8052541b0ce9e8d24c5ba82 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 30 Aug 2022 13:40:11 -0400 Subject: [PATCH 10/49] Add placeholder institution to fix draft-pdf CI --- doc/source/tracking/paper.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index a6959f66d..af8a3ed25 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -59,7 +59,7 @@ authors: affiliation: 13 # Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. - + affiliations: - name: University of New Hampshire, USA index: 1 @@ -67,33 +67,33 @@ affiliations: index: 2 - name: University of Colorado Boulder, USA index: 3 - - name: , USA + - name: Institution, USA index: 4 - name: University of Washington, USA index: 5 - - name: , USA + - name: Institution, USA index: 6 - - name: , USA + - name: Institution, USA index: 7 - - name: , USA + - name: Institution, USA index: 8 - - name: , USA + - name: Institution, USA index: 9 - name: University of Toronto, Canada index: 10 - - name: , USA + - name: Institution, USA index: 11 - - name: , USA + - name: Institution, USA index: 12 - - name: , USA + - name: Institution, USA index: 13 date: 1 September 2022 bibliography: icepyx_pubs.bib # Optional fields if submitting to a AAS journal too, see this blog post: # https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing -aas-doi: -aas-journal: +aas-doi: +aas-journal: --- # Summary From 45307dec37a6f0c8ca193d4102debfb78f0e383b Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 30 Aug 2022 13:45:45 -0400 Subject: [PATCH 11/49] Set folder path of paper.pdf to be same as paper.md --- .github/workflows/draft-pdf.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index c67efb6c3..7509d492a 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -20,4 +20,4 @@ jobs: # This is the output path where Pandoc will write the compiled # PDF. Note, this should be the same directory as the input # paper.md - path: paper.pdf \ No newline at end of file + path: doc/source/tracking/paper.pdf From ec8c83488d66ec62a7b89042c25d6ab2427b8733 Mon Sep 17 00:00:00 2001 From: aaarendt Date: Wed, 31 Aug 2022 15:39:16 -0700 Subject: [PATCH 12/49] add Anthony Arendt ORCID --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index af8a3ed25..1c2c72c41 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -17,6 +17,7 @@ authors: - name: Kelsey Bisson affiliation: 3 - name: Anthony Arendt + orcid: 0000-0003-0429-6905 affiliation: 4 - name: Shashank Bhushan affiliation: 4 From cba0460949c267f50fcac492682446fa9b17eed6 Mon Sep 17 00:00:00 2001 From: Kelsey Bisson <48059682+kelseybisson@users.noreply.github.com> Date: Thu, 8 Sep 2022 12:43:00 -0600 Subject: [PATCH 13/49] added orcid and affiliation --- doc/source/tracking/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 1c2c72c41..ccd8c806c 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -15,6 +15,7 @@ authors: orcid: 0000-0003-2354-1988 affiliation: 2 - name: Kelsey Bisson + orcid: 0000-0003-4230-3467 affiliation: 3 - name: Anthony Arendt orcid: 0000-0003-0429-6905 @@ -66,7 +67,7 @@ affiliations: index: 1 - name: The Ohio State University, USA index: 2 - - name: University of Colorado Boulder, USA + - name: Oregon State University, USA index: 3 - name: Institution, USA index: 4 From 1892020a8e3b4a738247a33f413fb5814c263ee7 Mon Sep 17 00:00:00 2001 From: Zach Fair <48361714+zachghiaccio@users.noreply.github.com> Date: Thu, 8 Sep 2022 16:44:16 -0400 Subject: [PATCH 14/49] Added ORCID, affiliation --- doc/source/tracking/paper.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index ccd8c806c..6bfc70aea 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -22,7 +22,8 @@ authors: affiliation: 4 - name: Shashank Bhushan affiliation: 4 - - name: Zach Fair + - name: Zachary Fair + orcid: 0000-0002-6047-1723 affiliation: 5 - name: Raphael Hagen affiliation: 4 @@ -73,7 +74,7 @@ affiliations: index: 4 - name: University of Washington, USA index: 5 - - name: Institution, USA + - name: NASA Goddard Space Flight Center, USA index: 6 - name: Institution, USA index: 7 From fb4cb37c154109430103a6976bc58dcbaac79e0c Mon Sep 17 00:00:00 2001 From: Zach Fair <48361714+zachghiaccio@users.noreply.github.com> Date: Thu, 8 Sep 2022 16:46:04 -0400 Subject: [PATCH 15/49] Fixed affiliation number --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 6bfc70aea..30a1b0e9c 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -24,7 +24,7 @@ authors: affiliation: 4 - name: Zachary Fair orcid: 0000-0002-6047-1723 - affiliation: 5 + affiliation: 6 - name: Raphael Hagen affiliation: 4 - name: Sarah Hall From 49ab3d4d2baabf4bbb6d67d152da21c0899c2661 Mon Sep 17 00:00:00 2001 From: liuzheng-arctic <51420076+liuzheng-arctic@users.noreply.github.com> Date: Thu, 8 Sep 2022 13:58:26 -0700 Subject: [PATCH 16/49] Create paper.md Add orcid for Zheng Liu. Changed the name of affiliation #4 to University of Washington instead of the generic "Institution" to be consistent with all other UW authors. --- doc/source/tracking/paper.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 30a1b0e9c..4d65862f8 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -24,7 +24,7 @@ authors: affiliation: 4 - name: Zachary Fair orcid: 0000-0002-6047-1723 - affiliation: 6 + affiliation: 5 - name: Raphael Hagen affiliation: 4 - name: Sarah Hall @@ -38,6 +38,7 @@ authors: - name: Tian Li affiliation: 8 - name: Zheng Liu + orcid: 0000-0003-4132-813 affiliation: 4 - name: Luis Lopez affiliation: 9 @@ -70,7 +71,7 @@ affiliations: index: 2 - name: Oregon State University, USA index: 3 - - name: Institution, USA + - name: University of Washington, USA index: 4 - name: University of Washington, USA index: 5 From 790fc86ec2fd5ed8c3b99ec7ed31d90f0e8e97eb Mon Sep 17 00:00:00 2001 From: Don Setiawan Date: Thu, 8 Sep 2022 16:09:49 -0700 Subject: [PATCH 17/49] Add orcid for Don Setiawan --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 4d65862f8..727ada5fe 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -47,6 +47,7 @@ authors: - name: Nitin Ravinder affiliation: 11 - name: Landung "Don" Setiawan + orcid: 0000-0002-1624-2667 affiliation: 4 - name: Trey Stafford affiliation: 9 From c931fddd7a2f516709b7916ce96c4493d1e4e826 Mon Sep 17 00:00:00 2001 From: Tian Li Date: Sat, 10 Sep 2022 18:56:16 +0100 Subject: [PATCH 18/49] added orcid and affiliation for Tian Li --- doc/source/tracking/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 727ada5fe..0e4c21599 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -36,6 +36,7 @@ authors: - name: Friedrich Knuth affiliation: 7 - name: Tian Li + orcid: 0000-0002-1577-4004 affiliation: 8 - name: Zheng Liu orcid: 0000-0003-4132-813 @@ -80,7 +81,7 @@ affiliations: index: 6 - name: Institution, USA index: 7 - - name: Institution, USA + - name: University of Bristol, UK index: 8 - name: Institution, USA index: 9 From 2b9bcc7cdf2e8008c802a433d3197ad55de26897 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 12 Sep 2022 12:32:20 -0400 Subject: [PATCH 19/49] add about IS2 and ref --- doc/source/tracking/icepyx_pubs.bib | 19 +++++++++++++++++-- doc/source/tracking/paper.md | 16 +++++++++++++--- 2 files changed, 30 insertions(+), 5 deletions(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index ce324e491..1c0b02334 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -96,8 +96,6 @@ @misc{js2019agu % ######### Articles citing icepyx ################ - - @article{Bisson:2021, author = {Bisson, K. M. and Cael, B. B.}, title = {How Are Under Ice Phytoplankton Related to Sea Ice in the Southern Ocean?}, @@ -136,3 +134,20 @@ @Article{Li:2020 URL = {https://tc.copernicus.org/articles/14/3629/2020/}, DOI = {10.5194/tc-14-3629-2020} } + + +% ######### Articles citing icepyx ################ + +@article{is2, +title = {The Ice, Cloud, and land Elevation Satellite-2 (ICESat-2): Science requirements, concept, and implementation}, +journal = {Remote Sensing of Environment}, +volume = {190}, +pages = {260-273}, +year = {2017}, +issn = {0034-4257}, +doi = {https://doi.org/10.1016/j.rse.2016.12.029}, +url = {https://www.sciencedirect.com/science/article/pii/S0034425716305089}, +author = {Thorsten Markus and Tom Neumann and Anthony Martino and Waleed Abdalati and Kelly Brunt and Beata Csatho and Sinead Farrell and Helen Fricker and Alex Gardner and David Harding and Michael Jasinski and Ron Kwok and Lori Magruder and Dan Lubin and Scott Luthcke and James Morison and Ross Nelson and Amy Neuenschwander and Stephen Palm and Sorin Popescu and CK Shum and Bob E. Schutz and Benjamin Smith and Yuekui Yang and Jay Zwally}, +keywords = {ICESat-2, Land ice, Sea ice, Vegetation, Climate change, Satellite mission}, +abstract = {The Ice, Cloud, and land Elevation Satellite (ICESat) mission used laser altimetry measurements to determine changes in elevations of glaciers and ice sheets, as well as sea ice thickness distribution. These measurements have provided important information on the response of the cryopshere (Earth's frozen surfaces) to changes in atmosphere and ocean condition. ICESat operated from 2003 to 2009 and provided repeat altimetry measurements not only to the cryosphere scientific community but also to the ocean, terrestrial and atmospheric scientific communities. The conclusive assessment of significant ongoing rapid changes in the Earth's ice cover, in part supported by ICESat observations, has strengthened the need for sustained, high accuracy, repeat observations similar to what was provided by the ICESat mission. Following recommendations from the National Research Council for an ICESat follow-on mission, the ICESat-2 mission is now under development for planned launch in 2018. The primary scientific aims of the ICESat-2 mission are to continue measurements of sea ice freeboard and ice sheet elevation to determine their changes at scales from outlet glaciers to the entire ice sheet, and from 10s of meters to the entire polar oceans for sea ice freeboard. ICESat carried a single beam profiling laser altimeter that produced ~70m diameter footprints on the surface of the Earth at ~150m along-track intervals. In contrast, ICESat-2 will operate with three pairs of beams, each pair separated by about 3km cross-track with a pair spacing of 90m. Each of the beams will have a nominal 17m diameter footprint with an along-track sampling interval of 0.7m. The differences in the ICESat-2 measurement concept are a result of overcoming some limitations associated with the approach used in the ICESat mission. The beam pair configuration of ICESat-2 allows for the determination of local cross-track slope, a significant factor in measuring elevation change for the outlet glaciers surrounding the Greenland and Antarctica coasts. The multiple beam pairs also provide improved spatial coverage. The dense spatial sampling eliminates along-track measurement gaps, and the small footprint diameter is especially useful for sea surface height measurements in the often narrow leads needed for sea ice freeboard and ice thickness retrievals. The ICESat-2 instrumentation concept uses a low energy 532nm (green) laser in conjunction with single-photon sensitive detectors to measure range. Combining ICESat-2 data with altimetry data collected since the start of the ICESat mission in 2003, such as Operation IceBridge and ESA's CryoSat-2, will yield a 15+ year record of changes in ice sheet elevation and sea ice thickness. ICESat-2 will also provide information of mountain glacier and ice cap elevations changes, land and vegetation heights, inland water elevations, sea surface heights, and cloud layering and optical thickness.} +} \ No newline at end of file diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 0e4c21599..13d321eaa 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -104,14 +104,24 @@ aas-journal: # Summary -icepyx is both a software library and a community composed of ICESat-2 data users, developers, maintainers, and the scientific community. +icepyx is both a software library and a community composed of ICESat-2 (NASA satellite) data users, developers, maintainers, and the scientific community. We are working together to develop a shared library of resources - including existing resources, new code, tutorials, and use-cases/examples - that simplify the process of querying, obtaining, analyzing, and manipulating ICESat-2 datasets to enable scientific discovery. # Statement of need -icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. icepyx also hopes to foster collaboration, open-science practices, and reproducible workflows by integrating and sharing resources. +icepyx aims to provide a clearinghouse for code, functionality to improve interoperability, documentation, examples, and educational resources that tackle disciplinary research questions while minimizing the amount of repeated effort across groups utilizing similar datasets. +icepyx also hopes to foster collaboration, open-science practices, and reproducible workflows by integrating and sharing resources. -icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. +The Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) [@is2] was launched by NASA in September 2018. +The laser altimeter on board the satellite emits green light and measures the time until each pulse is returned to the satellite's sensors. +This information is used to determine the surface height of the land, ice, snow, trees, water, clouds, etc. that the satellite is passing over. +The instruments provide close to 500 GB of data per day, allowing scientists to investigate the surface height of earth's features in unprecedented detail. + +icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. +At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. +This project combined and generalized the existing scripts into a unified framework, adding examples, documentation, and testing where necessary and making them accessible for everyone. +The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development practices. +icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications[@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. # Acknowledgements From 6db0d766953e089293ee8124d05c40b1e49833be Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 12 Sep 2022 12:41:39 -0400 Subject: [PATCH 20/49] fix author affiliation numbers to remove duplicate --- doc/source/tracking/paper.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 13d321eaa..a83854c94 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -58,11 +58,11 @@ authors: orcid: 0000-0002-6964-1194 affiliation: 4 - name: JP Swinski - affiliation: 12 + affiliation: 5 - name: Bruce Wallin affiliation: 9 - name: Learn2Pheonix - affiliation: 13 + affiliation: 12 # Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. @@ -75,9 +75,9 @@ affiliations: index: 3 - name: University of Washington, USA index: 4 - - name: University of Washington, USA - index: 5 - name: NASA Goddard Space Flight Center, USA + index: 5 + - name: Institution, USA index: 6 - name: Institution, USA index: 7 @@ -91,8 +91,6 @@ affiliations: index: 11 - name: Institution, USA index: 12 - - name: Institution, USA - index: 13 date: 1 September 2022 bibliography: icepyx_pubs.bib From 47478f4294e23ce8f0086706e7f002de2086f662 Mon Sep 17 00:00:00 2001 From: Friedrich Knuth Date: Tue, 13 Sep 2022 12:22:08 -0700 Subject: [PATCH 21/49] add Friedrich Knuth ORCID --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index a83854c94..8da62d7df 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -34,6 +34,7 @@ authors: - name: Tom Johnson affiliation: 6 - name: Friedrich Knuth + orcid: 0000-0003-1645-1984 affiliation: 7 - name: Tian Li orcid: 0000-0002-1577-4004 From eab8bf2266f9065bf66b5064cab308fb1e9c70d4 Mon Sep 17 00:00:00 2001 From: Raphael Hagen Date: Tue, 13 Sep 2022 12:47:05 -0700 Subject: [PATCH 22/49] Update paper.md --- doc/source/tracking/paper.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 8da62d7df..13165fd5d 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -25,8 +25,9 @@ authors: - name: Zachary Fair orcid: 0000-0002-6047-1723 affiliation: 5 - - name: Raphael Hagen - affiliation: 4 + - name: Norland Raphael Hagen + - orcid: 0000-0003-1994-1153 + affiliation: 6 - name: Sarah Hall affiliation: 1 - name: Scott Henderson @@ -78,7 +79,7 @@ affiliations: index: 4 - name: NASA Goddard Space Flight Center, USA index: 5 - - name: Institution, USA + - name: CarbonPlan, USA index: 6 - name: Institution, USA index: 7 From 0800b8c62fb4cd8699bcd2eedc7f1e115ed6c187 Mon Sep 17 00:00:00 2001 From: Shashank Bhushan Date: Tue, 13 Sep 2022 13:58:52 -0700 Subject: [PATCH 23/49] add orcid for Shashank --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 13165fd5d..be2db55af 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -21,6 +21,7 @@ authors: orcid: 0000-0003-0429-6905 affiliation: 4 - name: Shashank Bhushan + orcid: 0000-0003-3712-996X affiliation: 4 - name: Zachary Fair orcid: 0000-0002-6047-1723 From 9cd58a9a874f3128bf67807e288f0f77c140661a Mon Sep 17 00:00:00 2001 From: nitin-ravinder <86551841+nitin-ravinder@users.noreply.github.com> Date: Tue, 13 Sep 2022 22:03:48 +0100 Subject: [PATCH 24/49] Affiliation update for Nitin Ravinder --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index be2db55af..19271e574 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -90,7 +90,7 @@ affiliations: index: 9 - name: University of Toronto, Canada index: 10 - - name: Institution, USA + - name: University of Leeds, UK index: 11 - name: Institution, USA index: 12 From 737602f07e14b5b67a2d1e9118a9bace4286218f Mon Sep 17 00:00:00 2001 From: learn2phoenix <74139166+learn2phoenix@users.noreply.github.com> Date: Tue, 13 Sep 2022 17:26:19 -0400 Subject: [PATCH 25/49] adding name, affiliation, and orcid for learn2phoenix (#370) --- doc/source/tracking/paper.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 19271e574..cf571a93e 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -64,7 +64,8 @@ authors: affiliation: 5 - name: Bruce Wallin affiliation: 9 - - name: Learn2Pheonix + - name: Anubhav + orcid: 0000-0003-4017-2862 affiliation: 12 # Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. @@ -92,7 +93,7 @@ affiliations: index: 10 - name: University of Leeds, UK index: 11 - - name: Institution, USA + - name: University of Maryland, College Park, USA index: 12 date: 1 September 2022 bibliography: icepyx_pubs.bib From 19a03ec0a5ffa41b38a848d52dcd879bdd05da2d Mon Sep 17 00:00:00 2001 From: Scott Henderson Date: Tue, 13 Sep 2022 14:27:12 -0700 Subject: [PATCH 26/49] add scott henderson orcid (#371) --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index cf571a93e..ef115c0d1 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -32,6 +32,7 @@ authors: - name: Sarah Hall affiliation: 1 - name: Scott Henderson + orcid: 0000-0003-0624-4965 affiliation: 4 - name: Tom Johnson affiliation: 6 From 2eeb45af6b0124c2e83f805f6981c79c8f2fde7d Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 22 Sep 2022 15:22:37 -0400 Subject: [PATCH 27/49] remove authors who did not affirm authorship from list --- doc/source/tracking/paper.md | 49 +++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index ef115c0d1..baa2f8f0d 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -7,6 +7,7 @@ tags: - elevation - community - cloud + authors: - name: Jessica Scheick^[Corresponding author] # note this makes a footnote orcid: 0000-0002-3421-4459 @@ -29,13 +30,9 @@ authors: - name: Norland Raphael Hagen - orcid: 0000-0003-1994-1153 affiliation: 6 - - name: Sarah Hall - affiliation: 1 - name: Scott Henderson orcid: 0000-0003-0624-4965 affiliation: 4 - - name: Tom Johnson - affiliation: 6 - name: Friedrich Knuth orcid: 0000-0003-1645-1984 affiliation: 7 @@ -45,31 +42,23 @@ authors: - name: Zheng Liu orcid: 0000-0003-4132-813 affiliation: 4 - - name: Luis Lopez - affiliation: 9 - name: Romina Piunno - affiliation: 10 + affiliation: 9 - name: Nitin Ravinder - affiliation: 11 + affiliation: 10 - name: Landung "Don" Setiawan orcid: 0000-0002-1624-2667 affiliation: 4 - - name: Trey Stafford - affiliation: 9 - - name: Amy Steiker - affiliation: 9 - name: Tyler Sutterley orcid: 0000-0002-6964-1194 affiliation: 4 - name: JP Swinski affiliation: 5 - - name: Bruce Wallin - affiliation: 9 - name: Anubhav orcid: 0000-0003-4017-2862 - affiliation: 12 + affiliation: 11 -# Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the non-publication contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. +# Note: first three authors are driving the publication. Additional contributors/authors are listed in alphabetical order by last name. Anyone who also contributes substantially to preparing the JOSS submission will be moved into ABC order after the first three and before the "non-publication" contributors to icepyx. Non-responsive coauthors will be removed from the list since their permission to be included was not granted. affiliations: - name: University of New Hampshire, USA @@ -88,15 +77,13 @@ affiliations: index: 7 - name: University of Bristol, UK index: 8 - - name: Institution, USA - index: 9 - name: University of Toronto, Canada - index: 10 + index: 9 - name: University of Leeds, UK - index: 11 + index: 10 - name: University of Maryland, College Park, USA - index: 12 -date: 1 September 2022 + index: 11 +date: 23 September 2022 bibliography: icepyx_pubs.bib # Optional fields if submitting to a AAS journal too, see this blog post: @@ -131,7 +118,23 @@ icepyx is now a foundational tool for accessing and working with ICESat-2 data a We acknowledge funding support from NASA and the University of Washington eScience Institute. Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance in establishing this library and welcoming us to the open-source community. Amy Steiker, Mikala Beig, Nick Kotlinski, Luis Lopez, and many others at the National Snow and Ice Data Center (NSIDC) provide technical support and data access guidance. -The icepyx contributors list also includes many wonderful folks who shared ideas, provided mentoring, and embraced the opportunity to engage in open-science practices while working with ICESat-2 data products. +The icepyx contributors list also includes many wonderful folks who shared ideas, provided mentoring, embraced the opportunity to engage in open-science practices while working with ICESat-2 data products, and contributed to icepyx. + + - + classes_user_uml - + icepyx.core.Earthdata.Earthdata - -Earthdata - + +Earthdata + capability_url email netrc : NoneType -pswd : NoneType, str +pswd : str, NoneType session : Session uid - + login(attempts) icepyx.core.query.GenQuery - -GenQuery - - - + +GenQuery + + + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -download(verbose, path, session, restart) -get_avail(CMRparams, reqparams) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, session, geom_filepath) + +Granules + +avail : list +orderIDs : list + +download(verbose, path, session, restart) +get_avail(CMRparams, reqparams) +place_order(CMRparams, reqparams, subsetparams, verbose, subset, session, geom_filepath) icepyx.core.query.Query - -Query - -CMRparams -cycles -dataset -dates -end_time -file_vars -granules -order_vars -product -product_version -reqparams -spatial -spatial_extent -start_time -tracks - -avail_granules(ids, cycles, tracks, s3urls) -download_granules(path, verbose, subset, restart) -earthdata_login(uid, email, s3token) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +cycles +dataset +dates +end_time +file_vars +granules +order_vars +product +product_version +reqparams +spatial +spatial_extent +start_time +tracks + +avail_granules(ids, cycles, tracks, s3urls) +download_granules(path, verbose, subset, restart) +earthdata_login(uid, email, s3token) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams() +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - + +Icesat2Data + + + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + icepyx.core.APIformatting.Parameters - -Parameters - -fmted_keys -partype -poss_keys - -build_params() -check_req_values() -check_values() + +Parameters + +fmted_keys +partype +poss_keys + +build_params() +check_req_values() +check_values() icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.core.read.Read - -Read - -data_source : NoneType -is2catalog -vars - -load() + +Read + +data_source : NoneType +is2catalog +vars + +load() icepyx.core.spatial.Spatial - -Spatial - -extent_file -extent_type -spatial_extent - - + +Spatial + +extent_file +extent_type +spatial_extent + + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_sp_extent + + +_sp_extent icepyx.core.variables.Variables - -Variables - -path : NoneType -product : NoneType -wanted : NoneType, dict - -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +path : NoneType +product : NoneType +wanted : NoneType, dict + +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - -_file_vars + + +_file_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : str, NoneType -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): (hv.DynamicMap, hv.Layout) + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): (hv.DynamicMap, hv.Layout) From 115b47f629295115d1aaa2c9d7834276f8555f30 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 26 Sep 2022 16:28:40 -0400 Subject: [PATCH 35/49] rewrite sentence from code review --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 56c4076eb..b6a961df4 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -106,7 +106,7 @@ This information is used to determine the surface height of the land, ice, snow, The instrument provides close to 500 GB of data per day, allowing scientists to investigate the surface height of earth's features in unprecedented detail. icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of Washington in June 2019. -At the event, a clear need for a collaborative, shared community space that combined and generalized the tooling (including code and examples past, present, and future) written by Hackweek participants, ICESat-2 Science Team members, and the data user community. +At the event, there was a clear need for a collaborative, shared community space that combined and generalized the tools and materials written by past, present, and future Hackweek participants, ICESat-2 Science Team members, and the data user community. A unified framework of code and documentated examples for downloading, reading, and visualizing ICESat-2 data that is well tested makes it more accessible for everyone to use. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development best practices. icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications [@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. From a172c57b4047edba03bee3129237a27d8d4013e7 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 26 Sep 2022 20:33:23 +0000 Subject: [PATCH 36/49] GitHub action UML generation auto-update --- doc/source/user_guide/documentation/classes_dev_uml.svg | 8 ++++---- doc/source/user_guide/documentation/classes_user_uml.svg | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 9a49939e8..4c56ab53e 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -18,7 +18,7 @@ capability_url email netrc : NoneType -pswd : str, NoneType +pswd : NoneType, str session : Session uid @@ -162,9 +162,9 @@ Parameters -_fmted_keys : NoneType, dict +_fmted_keys : dict, NoneType _poss_keys : dict -_reqtype : str, NoneType +_reqtype : NoneType, str fmted_keys partype poss_keys @@ -221,7 +221,7 @@ _is2catalog : Catalog _out_obj : Dataset _pattern : str -_prod : NoneType, str +_prod : str, NoneType _read_vars _source_type : str data_source : NoneType diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index abd8d25b6..94056e11d 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -260,7 +260,7 @@ bbox : list cycles : NoneType date_range : NoneType -product : NoneType, str +product : str, NoneType tracks : NoneType generate_OA_parameters(): list From c357432f1df5c03e1cf04dc9dc9bdb958cd8d29f Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 26 Sep 2022 16:36:36 -0400 Subject: [PATCH 37/49] add more descriptive title --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index b6a961df4..dc5abc32d 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -1,5 +1,5 @@ --- -title: 'icepyx' +title: 'icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets' tags: - Python - ICESat-2 From d51e88b23df728de23956f803912b51ec52ef93c Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 6 Oct 2022 13:42:29 -0400 Subject: [PATCH 38/49] fix md formatting issue --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index dc5abc32d..ab4bf1984 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -28,7 +28,7 @@ authors: orcid: 0000-0002-6047-1723 affiliation: 5 - name: Norland Raphael Hagen - - orcid: 0000-0003-1994-1153 + orcid: 0000-0003-1994-1153 affiliation: 6 - name: Scott Henderson orcid: 0000-0003-0624-4965 From 5cdf5d810d2dcfb68de27b3c857de9e3722f6a30 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 6 Oct 2022 13:50:10 -0400 Subject: [PATCH 39/49] add joss bot recommended doi --- doc/source/tracking/icepyx_pubs.bib | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index 6c2e0cd00..9e037c6bc 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -35,11 +35,16 @@ @misc{2022_IS2-HW-tutorials url = {https://doi.org/10.5281/zenodo.6462479} } -@misc{js2021agu, -author = {Scheick, J. and Bisson, K. and Li, T. and Leong, W.J. and Arendt, A.}, +@article{js2021agu, +author = {Scheick, Jessica and Bisson, Kelsey and Li, Tian and Leong, Wei Ji and Arendt, Anthony}, note = {Abstract and poster (presented by Wei Ji Leong). American Geophysical Union Fall Meeting, New Orleans, LA, USA. 13-17 December 2021.}, title = {Collaborative Computational Resource Development around {ICESat-2} Data: the {icepyx} Community and Library}, -year = {2021}, +journal = {Earth and Space Science Open Archive}, +pages = {9}, +year = {2022}, +% for AGU Fall Meeting 2021 +DOI = {10.1002/essoar.10511316.1}, +url = {https://doi.org/10.1002/essoar.10511316.1}, comment = {abstract, poster}, } From 2d40766f4f284d0812a8b1b720c933befe566dfd Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Fri, 7 Oct 2022 11:07:40 -0400 Subject: [PATCH 40/49] add rest of Zheng's orcid ID --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index ab4bf1984..9bd189770 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -40,7 +40,7 @@ authors: orcid: 0000-0002-1577-4004 affiliation: 7 - name: Zheng Liu - orcid: 0000-0003-4132-813 + orcid: 0000-0003-4132-8136 affiliation: 4 - name: Romina Piunno affiliation: 8 From 88e5116ca5a0c3a5afe61fd8b6cc7c30e782d391 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 7 Nov 2022 13:52:22 -0500 Subject: [PATCH 41/49] Remove comment on AGU Fall Meeting 2021 citation Was causing issues with editorialbot at https://github.com/openjournals/joss-reviews/issues/4912#issuecomment-1305889442 --- doc/source/tracking/icepyx_pubs.bib | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index 57392d12c..49ea5f714 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -41,8 +41,7 @@ @article{js2021agu title = {Collaborative Computational Resource Development around {ICESat-2} Data: the {icepyx} Community and Library}, journal = {Earth and Space Science Open Archive}, pages = {9}, -year = {2022}, -% for AGU Fall Meeting 2021 +year = {2022}, DOI = {10.1002/essoar.10511316.1}, url = {https://doi.org/10.1002/essoar.10511316.1}, comment = {abstract, poster}, @@ -160,18 +159,18 @@ @article{is2 % ######### Research/Articles using (but not citing) icepyx ################ -@article{Sothe:2022, -title={Spatially Continuous Mapping of Forest Canopy Height in Canada by Combining GEDI and ICESat-2 with PALSAR and Sentinel}, -volume={14}, -ISSN={2072-4292}, -url={http://dx.doi.org/10.3390/rs14205158}, -DOI={10.3390/rs14205158}, -number={20}, -journal={Remote Sensing}, -publisher={MDPI AG}, -author={Sothe, Camile and Gonsamo, Alemu and Lourenço, Ricardo B. and Kurz, Werner A. and Snider, James}, -year={2022}, -month={Oct}, +@article{Sothe:2022, +title={Spatially Continuous Mapping of Forest Canopy Height in Canada by Combining GEDI and ICESat-2 with PALSAR and Sentinel}, +volume={14}, +ISSN={2072-4292}, +url={http://dx.doi.org/10.3390/rs14205158}, +DOI={10.3390/rs14205158}, +number={20}, +journal={Remote Sensing}, +publisher={MDPI AG}, +author={Sothe, Camile and Gonsamo, Alemu and Lourenço, Ricardo B. and Kurz, Werner A. and Snider, James}, +year={2022}, +month={Oct}, pages={5158}, note={Attribution to icepyx from 15 Oct 2022 Twitter post, https://twitter.com/rblourenco/status/1581320878511382528} } From 2ecdd27b10d08884f1daa227b5b1fb3262c70fb3 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 7 Mar 2023 16:54:14 -0500 Subject: [PATCH 42/49] is2 resource guide edits --- doc/source/tracking/icepyx_pubs.bib | 27 +++++++++++++++++++++++++++ doc/source/tracking/paper.md | 5 ++++- 2 files changed, 31 insertions(+), 1 deletion(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index 49ea5f714..1eb9bd1b3 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -174,3 +174,30 @@ @article{Sothe:2022 pages={5158}, note={Attribution to icepyx from 15 Oct 2022 Twitter post, https://twitter.com/rblourenco/status/1581320878511382528} } + + +% ######### Related Software ################ + +@software{jp_swinski_2023_7705009, + author = {JP Swinski and + Eric Lidwa and + Tyler Sutterley and + David Shean and + Joseph H Kennedy and + Scott Henderson}, + title = {ICESat2-SlideRule/sliderule: v2.1.0}, + month = mar, + year = 2023, + publisher = {Zenodo}, + version = {v2.1.0}, + doi = {10.5281/zenodo.7705009}, + url = {https://doi.org/10.5281/zenodo.7705009} +} + +@software{OA, + author = {Khalsa, S.J.S. and Borsa, A. and Nandigam, V. and others}, + title = {{OpenAltimetry} - rapid analysis and visualization of Spaceborne altimeter data}, + year = 2020, + publisher = {Earth Sci Inform}, + doi = {10.1007/s12145-020-00520-2}, + url = {https://openaltimetry.org/} diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 9bd189770..9f7341df8 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -109,7 +109,10 @@ icepyx began during the cryosphere-themed ICESat-2 Hackweek at the University of At the event, there was a clear need for a collaborative, shared community space that combined and generalized the tools and materials written by past, present, and future Hackweek participants, ICESat-2 Science Team members, and the data user community. A unified framework of code and documentated examples for downloading, reading, and visualizing ICESat-2 data that is well tested makes it more accessible for everyone to use. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development best practices. -icepyx is now a foundational tool for accessing and working with ICESat-2 data and is featured in multiple scientific publications [@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. + +icepyx is now a foundational tool for accessing and working with ICESat-2 data, responsible for nearly a quarter of all NASA data center granule downloads in 2022. The library is complimented by a series of other specialized tools for interacting with and obtaining ICESat-2 data. These include OpenAltimetry[@OA], a browser based web tool to visualize and download selected ICESat and ICESat-2 surface heights, SlideRule[@SR], a server-side framework to create cloud-based, on-demand customized data processing for ICESat-2 data, and multiple product-focused tools for scientific data analysis (e.g. PhoREAL, PhotonLabeler). These tools are described in more detail in the icepyx documentation's [ICESat-2 Resource Guide](https://icepyx.readthedocs.io/en/latest/community/resources.html). + +icepyx is also featured in multiple scientific publications [@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. # Acknowledgements From 553146624e01b9f92229e09d176f7e27e24db5bd Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 7 Mar 2023 16:58:43 -0500 Subject: [PATCH 43/49] fix bib file for build --- doc/source/tracking/icepyx_pubs.bib | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index 1eb9bd1b3..b2444767c 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -201,3 +201,4 @@ @software{OA publisher = {Earth Sci Inform}, doi = {10.1007/s12145-020-00520-2}, url = {https://openaltimetry.org/} +} \ No newline at end of file From 16de4bef2688598f03d245699105fa9e6268e35a Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 7 Mar 2023 17:15:28 -0500 Subject: [PATCH 44/49] try with @misc instead of @software in bib file --- doc/source/tracking/icepyx_pubs.bib | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index b2444767c..a0e6e6e16 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -178,7 +178,7 @@ @article{Sothe:2022 % ######### Related Software ################ -@software{jp_swinski_2023_7705009, +@misc{SR, author = {JP Swinski and Eric Lidwa and Tyler Sutterley and @@ -194,7 +194,7 @@ @software{jp_swinski_2023_7705009 url = {https://doi.org/10.5281/zenodo.7705009} } -@software{OA, +@misc{OA, author = {Khalsa, S.J.S. and Borsa, A. and Nandigam, V. and others}, title = {{OpenAltimetry} - rapid analysis and visualization of Spaceborne altimeter data}, year = 2020, From 62e284c61e40ab6bee79a18e21d28abffb7d83c8 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 16 Mar 2023 11:39:41 -0400 Subject: [PATCH 45/49] fix typo in doc/source/tracking/paper.md Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 9f7341df8..1eb86e96a 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -110,7 +110,7 @@ At the event, there was a clear need for a collaborative, shared community space A unified framework of code and documentated examples for downloading, reading, and visualizing ICESat-2 data that is well tested makes it more accessible for everyone to use. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development best practices. -icepyx is now a foundational tool for accessing and working with ICESat-2 data, responsible for nearly a quarter of all NASA data center granule downloads in 2022. The library is complimented by a series of other specialized tools for interacting with and obtaining ICESat-2 data. These include OpenAltimetry[@OA], a browser based web tool to visualize and download selected ICESat and ICESat-2 surface heights, SlideRule[@SR], a server-side framework to create cloud-based, on-demand customized data processing for ICESat-2 data, and multiple product-focused tools for scientific data analysis (e.g. PhoREAL, PhotonLabeler). These tools are described in more detail in the icepyx documentation's [ICESat-2 Resource Guide](https://icepyx.readthedocs.io/en/latest/community/resources.html). +icepyx is now a foundational tool for accessing and working with ICESat-2 data, responsible for nearly a quarter of all NASA data center granule downloads in 2022. The library is complemented by a series of other specialized tools for interacting with and obtaining ICESat-2 data. These include OpenAltimetry[@OA], a browser based web tool to visualize and download selected ICESat and ICESat-2 surface heights, SlideRule[@SR], a server-side framework to create cloud-based, on-demand customized data processing for ICESat-2 data, and multiple product-focused tools for scientific data analysis (e.g. PhoREAL, PhotonLabeler). These tools are described in more detail in the icepyx documentation's [ICESat-2 Resource Guide](https://icepyx.readthedocs.io/en/latest/community/resources.html). icepyx is also featured in multiple scientific publications [@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. From 2abf39234cdaab9309acb4b45df9635261d767cd Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 21 Mar 2023 11:31:45 +1300 Subject: [PATCH 46/49] Change Wei Ji's affiliation to DevSeed --- doc/source/tracking/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 1eb86e96a..87588d766 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -63,7 +63,7 @@ authors: affiliations: - name: University of New Hampshire, USA index: 1 - - name: The Ohio State University, USA + - name: Development Seed, USA index: 2 - name: Oregon State University, USA index: 3 From 7c0e306bb599c2526d37fbc66c50b847049c879b Mon Sep 17 00:00:00 2001 From: Romina Piunno Date: Wed, 29 Mar 2023 15:48:46 -0400 Subject: [PATCH 47/49] add orcid - Romina added ORCID for Romina Piunno --- doc/source/tracking/paper.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 87588d766..6d4530da0 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -43,6 +43,7 @@ authors: orcid: 0000-0003-4132-8136 affiliation: 4 - name: Romina Piunno + orcid: 0009-0000-1144-0915 affiliation: 8 - name: Nitin Ravinder affiliation: 9 From 85c88b1620b61bf51119a6d89cd484c1315d0cb8 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 6 Apr 2023 11:10:00 -0400 Subject: [PATCH 48/49] remove pdf draft generator required for submission --- .github/workflows/draft-pdf.yml | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 .github/workflows/draft-pdf.yml diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml deleted file mode 100644 index 7509d492a..000000000 --- a/.github/workflows/draft-pdf.yml +++ /dev/null @@ -1,23 +0,0 @@ -on: [push] - -jobs: - paper: - runs-on: ubuntu-latest - name: Paper Draft - steps: - - name: Checkout - uses: actions/checkout@v2 - - name: Build draft PDF - uses: openjournals/openjournals-draft-action@master - with: - journal: joss - # This should be the path to the paper within your repo. - paper-path: doc/source/tracking/paper.md - - name: Upload - uses: actions/upload-artifact@v1 - with: - name: paper - # This is the output path where Pandoc will write the compiled - # PDF. Note, this should be the same directory as the input - # paper.md - path: doc/source/tracking/paper.pdf From 2c0600b145ab25ab488eaf86c895f30ca700b174 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 11 Apr 2023 16:40:46 -0400 Subject: [PATCH 49/49] editorial updates --- doc/source/tracking/icepyx_pubs.bib | 16 ++++++++-------- doc/source/tracking/paper.md | 4 ++-- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/doc/source/tracking/icepyx_pubs.bib b/doc/source/tracking/icepyx_pubs.bib index a0e6e6e16..b2f8d2ed5 100644 --- a/doc/source/tracking/icepyx_pubs.bib +++ b/doc/source/tracking/icepyx_pubs.bib @@ -25,7 +25,7 @@ @misc{2022_IS2-HW-tutorials Joughin, Ian and Bisson, Kelsey and Sauthoff, Wilson}, -title = {ICESat-2 Hackweek Website}, +title = {{ICESat-2 Hackweek Website}}, month = apr, year = 2022, note = {If you use this book, please cite it as below.}, @@ -91,7 +91,7 @@ @misc{2020_IS2-HW-tutorials @misc{js2019agu, author = {Scheick, J. and Arendt, A. and Heagy, L. and Perez, F.}, note = {Abstract and poster. American Geophysical Union Fall Meeting, San Francisco, California, USA. 9-13 December 2019.}, -title = {{Introducing} icepyx, an open source {Python} library for obtaining and working with {ICESat-2} data}, +title = {Introducing {icepyx}, an open source {Python} library for obtaining and working with {ICESat-2} data}, year = {2019}, comment = {abstract,poster}, doi = {10.1002/essoar.10501423.1}, @@ -102,7 +102,7 @@ @misc{js2019agu @article{Bisson:2021, author = {Bisson, K. M. and Cael, B. B.}, -title = {How Are Under Ice Phytoplankton Related to Sea Ice in the Southern Ocean?}, +title = {How Are Under Ice Phytoplankton Related to Sea Ice in the {Southern Ocean}?}, journal = {Geophysical Research Letters}, volume = {48}, number = {21}, @@ -113,7 +113,7 @@ @article{Bisson:2021 } @inProceedings{Fernando:2021, - title = {Mapping the {{Diversity}} of {{Agricultural Systems}} in the {{Cuellaje Sector}}, {{Cotacachi}}, {{Ecuador Using ATL08}} for the {{ICESat-2 Mission}} and {{Machine Learning Techniques}}}, + title = {Mapping the Diversity of Agricultural Systems in the {{Cuellaje Sector, Cotacachi, Ecuador}} Using {{ATL08}} for the {{ICESat-2 Mission}} and Machine Learning Techniques}, booktitle = {Computational {{Science}} and {{Its Applications}} \textendash{} {{ICCSA}} 2021}, author = {Fernando, Garrido}, editor = {Gervasi, Osvaldo and Murgante, Beniamino and Misra, Sanjay and Garau, Chiara and Ble{\v c}i{\'c}, Ivan and Taniar, David and Apduhan, Bernady O. and Rocha, Ana Maria A. C. and Tarantino, Eufemia and Torre, Carmelo Maria}, @@ -129,7 +129,7 @@ @inProceedings{Fernando:2021 @Article{Li:2020, AUTHOR = {Li, T. and Dawson, G. J. and Chuter, S. J. and Bamber, J. L.}, -TITLE = {Mapping the grounding zone of Larsen~C Ice Shelf, Antarctica, from ICESat-2 laser altimetry}, +TITLE = {Mapping the grounding zone of {Larsen~C Ice Shelf, Antarctica}, from {ICESat-2} laser altimetry}, JOURNAL = {The Cryosphere}, VOLUME = {14}, YEAR = {2020}, @@ -143,7 +143,7 @@ @Article{Li:2020 % ######### Articles about ICESat-2 ################ @article{is2, -title = {The Ice, Cloud, and land Elevation Satellite-2 (ICESat-2): Science requirements, concept, and implementation}, +title = {The {Ice, Cloud, and land Elevation Satellite-2 (ICESat-2)}: Science requirements, concept, and implementation}, journal = {Remote Sensing of Environment}, volume = {190}, pages = {260-273}, @@ -160,7 +160,7 @@ @article{is2 @article{Sothe:2022, -title={Spatially Continuous Mapping of Forest Canopy Height in Canada by Combining GEDI and ICESat-2 with PALSAR and Sentinel}, +title={Spatially Continuous Mapping of Forest Canopy Height in {Canada} by Combining {GEDI} and {ICESat-2} with {PALSAR} and {Sentinel}}, volume={14}, ISSN={2072-4292}, url={http://dx.doi.org/10.3390/rs14205158}, @@ -185,7 +185,7 @@ @misc{SR David Shean and Joseph H Kennedy and Scott Henderson}, - title = {ICESat2-SlideRule/sliderule: v2.1.0}, + title = {{ICESat2-SlideRule}/sliderule: v2.1.0}, month = mar, year = 2023, publisher = {Zenodo}, diff --git a/doc/source/tracking/paper.md b/doc/source/tracking/paper.md index 6d4530da0..7a0e63690 100644 --- a/doc/source/tracking/paper.md +++ b/doc/source/tracking/paper.md @@ -111,14 +111,14 @@ At the event, there was a clear need for a collaborative, shared community space A unified framework of code and documentated examples for downloading, reading, and visualizing ICESat-2 data that is well tested makes it more accessible for everyone to use. The library and community continue to grow and evolve, adding new features and building scientific literacy in open-science, cloud computing, and collaborative development best practices. -icepyx is now a foundational tool for accessing and working with ICESat-2 data, responsible for nearly a quarter of all NASA data center granule downloads in 2022. The library is complemented by a series of other specialized tools for interacting with and obtaining ICESat-2 data. These include OpenAltimetry[@OA], a browser based web tool to visualize and download selected ICESat and ICESat-2 surface heights, SlideRule[@SR], a server-side framework to create cloud-based, on-demand customized data processing for ICESat-2 data, and multiple product-focused tools for scientific data analysis (e.g. PhoREAL, PhotonLabeler). These tools are described in more detail in the icepyx documentation's [ICESat-2 Resource Guide](https://icepyx.readthedocs.io/en/latest/community/resources.html). +icepyx is now a foundational tool for accessing and working with ICESat-2 data, responsible for nearly a quarter of all NASA data center granule downloads in 2022. The library is complemented by a series of other specialized tools for interacting with and obtaining ICESat-2 data. These include OpenAltimetry [@OA], a browser based web tool to visualize and download selected ICESat and ICESat-2 surface heights, SlideRule [@SR], a server-side framework to create cloud-based, on-demand customized data processing for ICESat-2 data, and multiple product-focused tools for scientific data analysis (e.g. PhoREAL, PhotonLabeler). These tools are described in more detail in the icepyx documentation's [ICESat-2 Resource Guide](https://icepyx.readthedocs.io/en/latest/community/resources.html). icepyx is also featured in multiple scientific publications [@Bisson:2021; @Fernando:2021; @Li:2020], presentations [@js2021agu; @js2020agu; @js2019agu], and educational events/Hackweeks [@2022_IS2-HW-tutorials; @2020_IS2-HW-tutorials]. # Acknowledgements We acknowledge funding support from NASA and the University of Washington eScience Institute. -Anthony Arendt, Fernando Perez, Lindsey Heagey, and the Pangeo team provided invaluable support and guidance in establishing this library and welcoming us to the open-source community. +Anthony Arendt, Fernando Perez, Lindsey Heagy, and the Pangeo team provided invaluable support and guidance in establishing this library and welcoming us to the open-source community. Amy Steiker, Mikala Beig, Nick Kotlinski, Luis Lopez, and many others at the National Snow and Ice Data Center (NSIDC) provide technical support and data access guidance. The icepyx contributors list also includes many wonderful folks who shared ideas, provided mentoring, embraced the opportunity to engage in open-science practices while working with ICESat-2 data products, and contributed to icepyx.