From f3b1a5f6955c26a37e61766798a780c915f84d5d Mon Sep 17 00:00:00 2001 From: Justin Bousquin Date: Tue, 22 Oct 2024 15:00:52 -0500 Subject: [PATCH 1/3] Create CITATION.cff Add JOSS citation --- CITATION.cff | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..eb6dcf2 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,36 @@ +CITATION.cff + +cff-version: "1.2.0" +authors: +- family-names: Bousquin + given-names: Justin + orcid: "https://orcid.org/0000-0001-5797-4322" +- family-names: Mullin + given-names: Cristina A. + orcid: "https://orcid.org/0000-0002-0615-6087" +doi: 10.5281/zenodo.13356847 +message: If you use this package, please cite our article in the + Journal of Open Source Software. +preferred-citation: + authors: + - family-names: Bousquin + given-names: Justin + orcid: "https://orcid.org/0000-0001-5797-4322" + - family-names: Mullin + given-names: Cristina A. + orcid: "https://orcid.org/0000-0002-0615-6087" + date-published: 2024-10-22 + doi: 10.21105/joss.07305 + issn: 2475-9066 + issue: 102 + journal: Journal of Open Source Software + publisher: + name: Open Journals + start: 7305 + title: "harmonize-wq: Standardize, clean and wrangle Water Quality + Portal data into more analytic-ready formats" + type: article + url: "https://joss.theoj.org/papers/10.21105/joss.07305" + volume: 9 +title: "harmonize-wq: Standardize, clean and wrangle Water Quality + Portal data into more analytic-ready formats" From d5129ab459bf14d387d23e520878ff384224fbfa Mon Sep 17 00:00:00 2001 From: Justin Bousquin Date: Tue, 22 Oct 2024 15:04:25 -0500 Subject: [PATCH 2/3] Update README.md Add JOSS badge/link to paper --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 2e222f1..40d05a1 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![test](https://github.com/USEPA/harmonize-wq/actions/workflows/test.yml/badge.svg)](https://github.com/USEPA/harmonize-wq/actions/workflows/test.yml) [![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/USEPA/harmonize-wq/main/pyproject.toml)](https://www.python.org/downloads/) [![pyOpenSci Peer-Reviewed](https://pyopensci.org/badges/peer-reviewed.svg)](https://github.com/pyOpenSci/software-review/issues/157) +[![DOI](https://joss.theoj.org/papers/10.21105/joss.07305/status.svg)](https://doi.org/10.21105/joss.07305) # harmonize-wq Standardize, clean, and wrangle Water Quality Portal data into more analytic-ready formats From 969d53b363c5aa9901d230c47bc8ca13acac9dfb Mon Sep 17 00:00:00 2001 From: Justin Bousquin Date: Thu, 31 Oct 2024 15:23:25 -0500 Subject: [PATCH 3/3] Add errors ignore so it doesn't default to error raise (failing). (#101) (#103) * Add errors ignore so it doesn't default to error raise (failing). THis change is needed because a new result has bad units (percent for secchi depth...). * Ignore pH errors (e.g., mV). This can be reverted if functionality is added in the future (see issue #102) --- demos/Harmonize_CapeCod_Detailed.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/demos/Harmonize_CapeCod_Detailed.ipynb b/demos/Harmonize_CapeCod_Detailed.ipynb index 42daa3e..abe03eb 100644 --- a/demos/Harmonize_CapeCod_Detailed.ipynb +++ b/demos/Harmonize_CapeCod_Detailed.ipynb @@ -1478,7 +1478,7 @@ "# Optional params: units='m', char_val='Depth, Secchi disk depth', out_col='Secchi', report=False)\n", "\n", "# We start by demonstrating on secchi disk depth (units default to m, keep intermediate fields, see report)\n", - "df = harmonize.harmonize(df, 'Depth, Secchi disk depth', intermediate_columns=True, report=True)" + "df = harmonize.harmonize(df, \"Depth, Secchi disk depth\", errors=\"ignore\", intermediate_columns=True, report=True)" ] }, { @@ -4110,7 +4110,7 @@ ], "source": [ "# pH, this time looking at a report\n", - "df = harmonize.harmonize(df, 'pH', report=True)" + "df = harmonize.harmonize(df, \"pH\", errors=\"ignore\", report=True)" ] }, {