From f66618a294fbe31e5c729946fc8a5365d4e61982 Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Wed, 3 Feb 2021 16:46:48 -0500 Subject: [PATCH 1/8] added - security scan - badge - contact - license file - disclaimer --- .github/workflows/secretScan.yml | 13 +++++++++++++ DESCRIPTION | 1 + LICENSE | 8 ++++++++ README.md | 26 +++++++++++++++++++++++++- 4 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/secretScan.yml create mode 100644 LICENSE diff --git a/.github/workflows/secretScan.yml b/.github/workflows/secretScan.yml new file mode 100644 index 00000000..51301a68 --- /dev/null +++ b/.github/workflows/secretScan.yml @@ -0,0 +1,13 @@ +name: gitleaks + +on: [push,pull_request] + +jobs: + gitleaks: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: '0' + - name: gitleaks-action + uses: zricethezav/gitleaks-action@master diff --git a/DESCRIPTION b/DESCRIPTION index 29d9f266..e86bf54c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,6 +3,7 @@ Type: Book Title: Synthetic Indicator Cataloque Description: Catalogue containing indicator used in the State of the Ecosystem Report and Beyond... Version: 1.0.0 +License: file LICENSE Depends: bookdown, rmarkdown, diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f9dec93c --- /dev/null +++ b/LICENSE @@ -0,0 +1,8 @@ +“Software code created by U.S. Government employees is not subject to +copyright in the United States (17 U.S.C. §105). The United States/Department +of Commerce reserve all rights to seek and obtain copyright +protection in countries other than the United States for Software authored +in its entirety by the Department of Commerce. To this end, the Department +of Commerce hereby grants to Recipient a royalty-free, nonexclusive +license to use, copy, and create derivative works of the Software outside +of the United States.” diff --git a/README.md b/README.md index adac0eeb..82b56280 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,31 @@ # [Synthetic Indicator Catalog](https://noaa-edab.github.io/catalog/) + +![gitleaks](https://github.com/NOAA-EDAB/LeMANS/workflows/gitleaks/badge.svg) + Catalog of indicators used in the State of the Ecosystem reports and other ecosystem assessment products. This book is in development. +## Contact + +| [kimberly-bastille](https://github.com/kimberly-bastille) +| ----------------------------------------------------------------------------------------------- +| [![]https://avatars.githubusercontent.com/u/39955661?s=100&u=b65aaafd27d4c925988755e61e497e2e7d573622&v=4)](https://github.com/kimberly-bastille) | + + + +#### Legal disclaimer -*This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.* \ No newline at end of file +*This repository is a scientific product and is not official +communication of the National Oceanic and Atmospheric Administration, or +the United States Department of Commerce. All NOAA GitHub project code +is provided on an ‘as is’ basis and the user assumes responsibility for +its use. Any claims against the Department of Commerce or Department of +Commerce bureaus stemming from the use of this GitHub project will be +governed by all applicable Federal law. Any reference to specific +commercial products, processes, or services by service mark, trademark, +manufacturer, or otherwise, does not constitute or imply their +endorsement, recommendation or favoring by the Department of Commerce. +The Department of Commerce seal and logo, or the seal and logo of a DOC +bureau, shall not be used in any manner to imply endorsement of any +commercial product or activity by DOC or the United States Government.* From f1d30faf35fbf68f09b16258e6239574e89b2f83 Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Wed, 3 Feb 2021 16:51:55 -0500 Subject: [PATCH 2/8] fix contact --- README.md | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 82b56280..fe102abc 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,30 @@ +--- +editor_options: + markdown: + wrap: 72 +--- + # [Synthetic Indicator Catalog](https://noaa-edab.github.io/catalog/) ![gitleaks](https://github.com/NOAA-EDAB/LeMANS/workflows/gitleaks/badge.svg) -Catalog of indicators used in the State of the Ecosystem reports and other ecosystem assessment products. +Catalog of indicators used in the State of the Ecosystem reports and +other ecosystem assessment products. -This book is in development. +This book is in development. ## Contact -| [kimberly-bastille](https://github.com/kimberly-bastille) -| ----------------------------------------------------------------------------------------------- -| [![]https://avatars.githubusercontent.com/u/39955661?s=100&u=b65aaafd27d4c925988755e61e497e2e7d573622&v=4)](https://github.com/kimberly-bastille) | - - +| [kimberly-bastille](https://github.com/kimberly-bastille) +|-------------------------------- +| [![](https://avatars.githubusercontent.com/u/39955661?s=100&u=b65aaafd27d4c925988755e61e497e2e7d573622&v=4)](https://github.com/kimberly-bastille) | #### Legal disclaimer *This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code -is provided on an ‘as is’ basis and the user assumes responsibility for +is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific From a62739c1f7f1986b32a2c7cb2f4b877e9702bd7f Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Wed, 3 Feb 2021 17:07:23 -0500 Subject: [PATCH 3/8] typo in badge path --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fe102abc..157de7f1 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ editor_options: # [Synthetic Indicator Catalog](https://noaa-edab.github.io/catalog/) -![gitleaks](https://github.com/NOAA-EDAB/LeMANS/workflows/gitleaks/badge.svg) +![gitleaks](https://github.com/NOAA-EDAB/catalog/workflows/gitleaks/badge.svg) Catalog of indicators used in the State of the Ecosystem reports and other ecosystem assessment products. From b837613d23e42a611d0632dd4e01e13c6a296c4a Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Mon, 18 Sep 2023 09:28:19 -0400 Subject: [PATCH 4/8] packages update in bib --- packages.bib | 51 +++++++++++++++++++++------------------------------ 1 file changed, 21 insertions(+), 30 deletions(-) diff --git a/packages.bib b/packages.bib index 161c6a3f..d0ab1c27 100644 --- a/packages.bib +++ b/packages.bib @@ -35,7 +35,7 @@ @Manual{R-dplyr title = {dplyr: A Grammar of Data Manipulation}, author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller}, year = {2022}, - note = {R package version 1.0.10}, + note = {R package version 1.0.9}, url = {https://CRAN.R-project.org/package=dplyr}, } @@ -43,7 +43,7 @@ @Manual{R-DT title = {DT: A Wrapper of the JavaScript Library DataTables}, author = {Yihui Xie and Joe Cheng and Xianying Tan}, year = {2022}, - note = {R package version 0.23}, + note = {R package version 0.24}, url = {https://github.com/rstudio/DT}, } @@ -66,15 +66,15 @@ @Manual{R-ggiraph title = {ggiraph: Make ggplot2 Graphics Interactive}, author = {David Gohel and Panagiotis Skintzos}, year = {2022}, - note = {R package version 0.8.2}, + note = {R package version 0.8.3}, url = {https://davidgohel.github.io/ggiraph/}, } @Manual{R-ggplot2, title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics}, author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington}, - year = {2022}, - note = {R package version 3.4.0}, + year = {2023}, + note = {R package version 3.4.2}, url = {https://CRAN.R-project.org/package=ggplot2}, } @@ -115,7 +115,7 @@ @Manual{R-knitr title = {knitr: A General-Purpose Package for Dynamic Report Generation in R}, author = {Yihui Xie}, year = {2022}, - note = {R package version 1.39}, + note = {R package version 1.41}, url = {https://yihui.org/knitr/}, } @@ -138,9 +138,8 @@ @Manual{R-miniUI @Manual{R-patchwork, title = {patchwork: The Composer of Plots}, author = {Thomas Lin Pedersen}, - year = {2020}, - note = {R package version 1.1.1}, - url = {https://CRAN.R-project.org/package=patchwork}, + year = {2023}, + note = {https://patchwork.data-imaginist.com}, } @Manual{R-permute, @@ -153,9 +152,9 @@ @Manual{R-permute @Manual{R-purrr, title = {purrr: Functional Programming Tools}, - author = {Hadley Wickham and Lionel Henry}, - year = {2022}, - note = {R package version 1.0.0}, + author = {Lionel Henry and Hadley Wickham}, + year = {2020}, + note = {R package version 0.3.4}, url = {https://CRAN.R-project.org/package=purrr}, } @@ -187,7 +186,7 @@ @Manual{R-rmarkdown title = {rmarkdown: Dynamic Documents for R}, author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone}, year = {2022}, - note = {R package version 2.14}, + note = {R package version 2.16}, url = {https://CRAN.R-project.org/package=rmarkdown}, } @@ -199,14 +198,6 @@ @Manual{R-rpart url = {https://CRAN.R-project.org/package=rpart}, } -@Manual{R-rticles, - title = {rticles: Article Formats for R Markdown}, - author = {JJ Allaire and Yihui Xie and Christophe Dervieux and {R Foundation} and Hadley Wickham and {Journal of Statistical Software} and Ramnath Vaidyanathan and {Association for Computing Machinery} and Carl Boettiger and {Elsevier} and Karl Broman and Kirill Mueller and Bastiaan Quast and Randall Pruim and Ben Marwick and Charlotte Wickham and Oliver Keyes and Miao Yu and Daniel Emaasit and Thierry Onkelinx and Alessandro Gasparini and Marc-Andre Desautels and Dominik Leutnant and {MDPI} and {Taylor and Francis} and Oğuzhan Öğreden and Dalton Hance and Daniel Nüst and Petter Uvesten and Elio Campitelli and John Muschelli and Alex Hayes and Zhian N. Kamvar and Noam Ross and Robrecht Cannoodt and Duncan Luguern and David M. Kaplan and Sebastian Kreutzer and Shixiang Wang and Jay Hesselberth and Rob Hyndman}, - year = {2022}, - note = {R package version 0.24}, - url = {https://github.com/rstudio/rticles}, -} - @Manual{R-servr, title = {servr: A Simple HTTP Server to Serve Static Files or Dynamic Documents}, author = {Yihui Xie}, @@ -219,7 +210,7 @@ @Manual{R-sf title = {sf: Simple Features for R}, author = {Edzer Pebesma}, year = {2022}, - note = {R package version 1.0-8}, + note = {R package version 1.0-7}, url = {https://CRAN.R-project.org/package=sf}, } @@ -234,16 +225,16 @@ @Manual{R-sp @Manual{R-stringr, title = {stringr: Simple, Consistent Wrappers for Common String Operations}, author = {Hadley Wickham}, - year = {2019}, - note = {R package version 1.4.0}, + year = {2022}, + note = {R package version 1.5.0}, url = {https://CRAN.R-project.org/package=stringr}, } @Manual{R-tibble, title = {tibble: Simple Data Frames}, author = {Kirill Müller and Hadley Wickham}, - year = {2022}, - note = {R package version 3.1.8}, + year = {2023}, + note = {R package version 3.2.1}, url = {https://CRAN.R-project.org/package=tibble}, } @@ -251,15 +242,15 @@ @Manual{R-tidyr title = {tidyr: Tidy Messy Data}, author = {Hadley Wickham and Maximilian Girlich}, year = {2022}, - note = {R package version 1.2.1}, + note = {R package version 1.2.0}, url = {https://CRAN.R-project.org/package=tidyr}, } @Manual{R-tidyverse, title = {tidyverse: Easily Install and Load the Tidyverse}, author = {Hadley Wickham}, - year = {2022}, - note = {R package version 1.3.2}, + year = {2021}, + note = {R package version 1.3.1}, url = {https://CRAN.R-project.org/package=tidyverse}, } @@ -275,7 +266,7 @@ @Manual{R-webshot title = {webshot: Take Screenshots of Web Pages}, author = {Winston Chang}, year = {2022}, - note = {R package version 0.5.3}, + note = {R package version 0.5.4}, url = {https://CRAN.R-project.org/package=webshot}, } From bc8f5db9171fcef94fe1a4bed34ce813d42ed31b Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Mon, 18 Sep 2023 09:31:41 -0400 Subject: [PATCH 5/8] update readme to include Brandon as contact --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 157de7f1..05db9562 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,9 @@ This book is in development. ## Contact -| [kimberly-bastille](https://github.com/kimberly-bastille) +| [Brandon-Beltz](https://github.com/BBeltz1) |-------------------------------- -| [![](https://avatars.githubusercontent.com/u/39955661?s=100&u=b65aaafd27d4c925988755e61e497e2e7d573622&v=4)](https://github.com/kimberly-bastille) | +| [![](https://avatars.githubusercontent.com/u/136381970?s=100&u=b65aaafd27d4c925988755e61e497e2e7d573622&v=4)](https://github.com/BBeltz1) | #### Legal disclaimer From 1a40c693ea3b16bee88a6f53cbb7e8a789fd8725 Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Mon, 18 Sep 2023 09:37:22 -0400 Subject: [PATCH 6/8] changed gitleaks license to free version --- .github/workflows/secretScan.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/secretScan.yml b/.github/workflows/secretScan.yml index 51301a68..30e55ea4 100644 --- a/.github/workflows/secretScan.yml +++ b/.github/workflows/secretScan.yml @@ -10,4 +10,4 @@ jobs: with: fetch-depth: '0' - name: gitleaks-action - uses: zricethezav/gitleaks-action@master + uses: zricethezav/gitleaks-action@v1.6.0 From 5737f28cf75dbfa1c58349a914735dfe67db806d Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Mon, 18 Sep 2023 15:32:35 -0400 Subject: [PATCH 7/8] catalog submission v2 Second iteration of the catalog submission issue template. Removed fields that were redundant between catalog and techdoc. Added fields for written sections of catalog. --- .github/ISSUE_TEMPLATE/catalog_submission.yml | 75 ++++++++++--------- 1 file changed, 41 insertions(+), 34 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/catalog_submission.yml b/.github/ISSUE_TEMPLATE/catalog_submission.yml index 9a5d6dc1..1e04b2c4 100644 --- a/.github/ISSUE_TEMPLATE/catalog_submission.yml +++ b/.github/ISSUE_TEMPLATE/catalog_submission.yml @@ -40,6 +40,46 @@ body: value: "Ex: The data presented here are average annual sea-surface temperatures from PSL OISST on the Northeast Continental Shelf." validations: required: true + - type: textarea + id: indicator_intro + attributes: + label: Introduction to Indicator + description: Please introduce the indicator within an appropriate context. Proceed as though this were a short summary of a typical introduction section in a paper. + value: + validations: + required: false + - type: textarea + id: indicator_results + attributes: + label: Key Results and Visualization + description: Please describe the results and/or visualizations of this indicator. Proceed as though this were a short summary of a typical results section in a paper. + value: + validations: + required: false + - type: textarea + id: indicator_implications + attributes: + label: Implications + description: Please describe the implications of this indicator. Proceed as though this were a short summary of a typical discussion section in a paper. + value: + validations: + required: false + - type: input + id: spatial_scale + attributes: + label: Spatial Scale + description: Please briefly describe the spatial scale of the indicator. + placeholder: ex. by EPU and full shelf. + validations: + required: false + - type: input + id: temporal_scale + attributes: + label: Temporal Scale + description: Please briefly describe the temporal scale of the indicator. + placeholder: ex. Spring (January-June), Fall (July-December), Annual. + validations: + required: false - type: checkboxes id: synthesis_theme attributes: @@ -114,37 +154,4 @@ body: description: If source data are NOT publicly available, what are the procedures for accessing the data? placeholder: Ex. Please email your.email@noaa.gov for further information and queries of X indicator source data. validations: - required: false - - type: markdown - attributes: - value: "## Methods" - - type: markdown - attributes: - value: | - In the following sections, please outline the methods used for these indicator data. Please include any documentation when available (i.e. links to code, published works, etc). If easier, you may include a write up of your methods in a separate document and upload that file below. - - type: textarea - id: data_source - attributes: - label: Data Source(s) - description: Describe data sources here, with links wherever applicable. - validations: - required: true - - type: textarea - id: data_processing - attributes: - label: Data Processing - description: How were data processed? At minimum, please include a text description of the processing steps. Code may be uploaded as a supporting file below. If code is published elsewhere, please provide a link. - validations: - required: false - - type: textarea - id: data_analysis - attributes: - label: Data Analysis - description: How were the data analyzed? Please provide a description of analytical methods, upload any relevant code and/or link to appropriate sources. At minimum, please include a text description of the analytical steps. Code may be uploaded as a supporting file below. - validations: - required: false - - type: textarea - id: bibliography - attributes: - label: Bibiography - description: Use this space to enter citations for above fields, preferably in BibTeX format. Otherwise, please upload a bibliography as a supporting file below. + required: false \ No newline at end of file From 8b880a7b7396d73f3221becacd53eae4df333d12 Mon Sep 17 00:00:00 2001 From: Brandon Beltz - NOAA Affiliate <136381970+BBeltz1@users.noreply.github.com> Date: Mon, 18 Sep 2023 15:38:53 -0400 Subject: [PATCH 8/8] catalog submission v2.1 Split the description of written catalog sections so that the entry boxes are populated. --- .github/ISSUE_TEMPLATE/catalog_submission.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/catalog_submission.yml b/.github/ISSUE_TEMPLATE/catalog_submission.yml index 1e04b2c4..7c00de19 100644 --- a/.github/ISSUE_TEMPLATE/catalog_submission.yml +++ b/.github/ISSUE_TEMPLATE/catalog_submission.yml @@ -44,24 +44,24 @@ body: id: indicator_intro attributes: label: Introduction to Indicator - description: Please introduce the indicator within an appropriate context. Proceed as though this were a short summary of a typical introduction section in a paper. - value: + description: Please introduce the indicator within an appropriate context. + value: "Proceed as though this were a short summary of a typical introduction section in a paper." validations: required: false - type: textarea id: indicator_results attributes: label: Key Results and Visualization - description: Please describe the results and/or visualizations of this indicator. Proceed as though this were a short summary of a typical results section in a paper. - value: + description: Please describe the results and/or visualizations of this indicator. + value: "Proceed as though this were a short summary of a typical results section in a paper." validations: required: false - type: textarea id: indicator_implications attributes: label: Implications - description: Please describe the implications of this indicator. Proceed as though this were a short summary of a typical discussion section in a paper. - value: + description: Please describe the implications of this indicator. + value: "Proceed as though this were a short summary of a typical discussion section in a paper." validations: required: false - type: input