Merge pull request #82 from USEPA/pyOpenSci-review

* Update README.md with badges * Update README.md Docs link and format issues link * Update domains.py TADA repo is now EPATADA to be unique for CRAN * Update broken link * Update Harmonize_Pensacola.Rmd * remove full path * Update requirements.txt Be more specific about lowest version * Update requirements.txt pin older version (32 vs 64 changes for dtype) * Update domains.py Interesting new domain was added... * Minor edits to text * Fix plot * Install from deve version not pinned release (one less thing to update) * Resolve first error when knit locally * Comment out some of the option 2 code so it doesn't run when knit-ing. Open to better options of how to format it as code but not always run it.. * First attempt to render the rmd in R (i.e. run the python code in R vignette) * Update test_r.yaml Try without renv, fixed typo. * Update test_r.yaml Switch from pip to conda (required of reticulate) * Update test_r.yaml Try setting up env using reticulate instead of conda (since conda-incubator is currently restricted) * Update test_r.yaml Combine install/run so env is not lost * Update test_r.yaml update env name * Update test_r.yaml Combine again without typo * Update test_r.yaml use miniconda_install() (note before I was setting up venv) * Update test_r.yaml install dev package from repo... for tests this should use the currently checked out instead, but just trying to get it working. * Update test_r.yaml Not sure why now it was case sensitive... * Update test_r.yaml pytest already check tests in test.yml, no need to run it a second time here. * Update test_r.yaml Skip unbutu, run all windows (conda) * Update test_r.yaml Trying on ubuntu again * Update test_r.yaml Try on older ubuntu version. * Update test_r.yaml bump action version up (getting warnings) * Update test_r.yaml Drop Ubuntu. Fix where python version is set from the matrix. Conda create with python version from matrix. * Update test_r.yaml Try setting var from matrix using with since it seemed to cut out 3.1* for 3.10. * Update test_r.yaml Try again (hoping it won't truncate python 3.1x this time. * Update test_r.yaml try as sting? * Dynamic config pyproject.toml Use dynamic to specify depends from requirements.txt. This should be more maintainable. and may resolve some of the install issues reveries were having. setuptools>=61.0 already required. * Update test_r.yaml Upload artifact at end to examine rendered html * Update artifact test_r.yaml Based on examples on repo * Update test_r.yaml * Update test_r.yaml Only upload on one runner (win 3.11 * Wordsmith Harmonize_Pensacola.Rmd Updated text to be more accurate with how reticulate can be used * separators Harmonize_Pensacola.Rmd No separators for list to conda --------- Co-authored-by: Romain Caneill <[email protected]> Co-authored-by: cristinamullin <[email protected]> * Add masked result to show how ['ResultMeasure/MeasureUnitCode'] == 'deg F' changed. Re-ran all results to update. Closes #73 * Update contributing.rst Adding example code for dev env. Closes #63 --------- Co-authored-by: Romain Caneill <[email protected]> Co-authored-by: cristinamullin <[email protected]>
USEPA · Jul 5, 2024 · 3f3082d · 3f3082d
2 parents 054c2a5 + 4d1dd8c
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diff --git a/README.md b/README.md
@@ -1,6 +1,8 @@
 [![PyPi](https://img.shields.io/pypi/v/harmonize-wq.svg)](https://pypi.python.org/pypi/harmonize-wq)
 [![Documentation Status](https://github.com/USEPA/harmonize-wq/actions/workflows/documentation_deploy.yaml/badge.svg)](https://github.com/USEPA/harmonize-wq/actions/workflows/documentation_deploy.yaml)
-
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![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](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
 # harmonize-wq
 Standardize, clean, and wrangle Water Quality Portal data into more analytic-ready formats
 
@@ -15,7 +17,7 @@ Recognizing the definition of analysis-ready varies depending on the analysis, t
 
 Domain experts must decide what data meets their quality standards for data comparability and any thresholds for acceptance or rejection.
 
-For more complete tutorial information, see: [demos](https://github.com/USEPA/harmonize-wq/tree/main/demos)
+For more complete, documentsion see [docs](https://usepa.github.io/harmonize-wq/index.html). For more complete tutorial information, see: [demos](https://github.com/USEPA/harmonize-wq/tree/main/demos)
 
 ## Quick Start
 
@@ -111,9 +113,7 @@ Temperature | Result | ResultMeasureValue, ResultMeasure/MeasureUnitCode | stand
 QA_Temperature | QA | NA | harmonization processing quality issues
 
 ## Issue Tracker
-harmonize_wq is under development. Please report any bugs and enhancement ideas using the issue track:
-
-https://github.com/USEPA/harmonize-wq/issues
+harmonize_wq is under development. Please report any bugs and enhancement ideas using [issues](https://github.com/USEPA/harmonize-wq/issues)
 
 
 ## Disclaimer

diff --git a/contributing.rst b/contributing.rst
@@ -53,11 +53,33 @@ There might be multiple reasons for this but these are some of the most common:
 Development environment setup
 -----------------------------
 
-- pip install the latest development version of the package from `GitHub <https://github.com/USEPA/harmonize-wq>`_
-- Install the requirements for the development environment by pip installing the additional requirements-dev.txt file.
+- pip install the latest development version of the package from `GitHub <https://github.com/USEPA/harmonize-wq>`_, e.g.,:
+
+.. code-block:: python3
+   
+    pip install git+https://github.com/USEPA/harmonize-wq.git
+
+
+- Install the requirements for the development environment by pip installing the additional requirements-dev.txt file, e.g.,:
+
+.. code-block:: python3
+   
+    pip install -r requirements_dev.txt
+
+docs are built using sphinx, by navigating to the doc folder and making the desired type (html):
+
+.. code-block:: python3
+   
+  cd doc
+  make html
+
+
+tests are run using pytest, e.g., 
+
+.. code-block:: python3
+   
+  pytest harmonize_wq
 
-docs are built using sphinx
-tests are run using pytest
 
 There are workflows using GitHub actions for both docs and tests to help avoid 'it worked on my machine' type development issues.
 

diff --git a/demos/Harmonize_CapeCod_Detailed.ipynb b/demos/Harmonize_CapeCod_Detailed.ipynb
diff --git a/harmonize_wq/domains.py b/harmonize_wq/domains.py
@@ -10,7 +10,7 @@
 
 
 BASE_URL = 'https://cdx.epa.gov/wqx/download/DomainValues/'
-TADA_DATA_URL = r'https://raw.githubusercontent.com/USEPA/TADA/'
+TADA_DATA_URL = r'https://raw.githubusercontent.com/USEPA/EPATADA/'
 
 UNITS_REPLACE = {'Secchi': {},
                  'DO': {'%': 'percent'},