v0.7.4 (#31)

* Removed scardb/phyto module. Removed unecessary dependencies. Updated to 7.4.0 * Updated tests to fix warnings * Changed mapping to use months instead of seasons for mapbox. * Updated changelog * Removed socket.dev badge. Added badge for coverage to testing workflow. * Made tests run for every push * Coverage badge bugfix * Coverage badge bugfix * Coverage badge bugfix * Coverage badge bugfix * Coverage badge bugfix * Coverage badge bugfix
nikothomas · Aug 11, 2024 · a565fc7 · a565fc7
1 parent eaf19b4
commit a565fc7
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diff --git a/.github/workflows/sphinxdocs.yml b/.github/workflows/sphinxdocs.yml
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -4,7 +4,7 @@ on:
   pull_request:
     branches: [main]
   push:
-    branches: [main]
+    branches: ['*']
 
 jobs:
   run-with-coverage:
@@ -59,3 +59,21 @@ jobs:
         with:
           name: coverage-report
           path: htmlcov
+
+      - name: Get coverage percentage
+        id: get-coverage
+        run: |
+          coverage=$(poetry run pytest --cov=ctdfjorder --cov-report=term | grep TOTAL | awk '{print $4}' | sed 's/%//')
+          echo "ANSWER=$coverage" >> $GITHUB_ENV
+
+      - name: Create the Badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: 5ceb7e714da5151b751f668c4cc49013
+          filename: answer.json
+          label: Coverage
+          message: ${{ env.ANSWER }} %
+          valColorRange: ${{ env.ANSWER }}
+          maxColorRange: 100
+          minColorRange: 0
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13293668.svg#2)](https://doi.org/10.5281/zenodo.13293668)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13293665.svg#3)](https://doi.org/10.5281/zenodo.13293665)
 ![Tests](https://github.com/nikothomas/ctdfjorder/actions/workflows/tests.yml/badge.svg?branch=main)
-[![PyPI version](https://badge.fury.io/py/ctdfjorder.svg#2)](https://badge.fury.io/py/ctdfjorder)
-[![Socket Badge](https://socket.dev/api/badge/pypi/package/ctdfjorder/0.7.3#2)](https://socket.dev/pypi/package/ctdfjorder/overview/0.7.32)
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/nikothomas/5ceb7e714da5151b751f668c4cc49013/raw/answer.json)
+[![PyPI version](https://badge.fury.io/py/ctdfjorder.svg#3)](https://badge.fury.io/py/ctdfjorder)
 
 <p style=text-align:center;>
   <img src="https://raw.githubusercontent.com/nikothomas/ctdfjorder/main/logo.png" alt="CTDFjorder Logo"/>
@@ -15,6 +15,7 @@ Documentation: [Read the docs](https://nikothomas.github.io/ctdfjorder/)
 - [<code>🚀 Usage</code>](#-usage)
 - [<code>⚠️ Issues</code>](#-issues)
 - [<code>📝 License</code>](#-license)
+- [<code>📑 Citing CTDFjorder</code>](#-license)
 - [<code>📢 Acknowledgments</code>](#-acknowledgments)
 
 ## ⭐ Features
@@ -49,8 +50,11 @@ If you encounter an issue while running or using CTDFjorder, please submit a rep
 ## 📝 License
 CTDFjorder is released under the MIT License.
 
+## 📑 Citing CTDFjorder
+Citation information for CTDFjorder can be found here [zenodo.13293665](https://dx.doi.org10/zenodo.13293665>).
+
 ## 📢 Acknowledgments
-CTDFjorder was developed for the [Fjord Phyto](https://fjordphyto.ucsd.edu) project. The gsw library was used for certain dervied calculations.
+CTDFjorder was developed for the [Fjord Phyto](https://fjordphyto.ucsd.edu) project. The [GSW-python](https://github.com/TEOS-10/GSW-Python) library was used for certain dervied calculations.
 
 ## Citations
 McDougall, T. J., & Barker, P. M. (2011). Getting started with TEOS-10 and the Gibbs Seawater (GSW) Oceanographic Toolbox. SCOR/IAPSO WG127.

diff --git a/ctdfjorder/CTD.py b/ctdfjorder/CTD.py
@@ -314,11 +314,11 @@ def remove_upcasts(self) -> None:
         self._is_empty(CTD.remove_upcasts.__name__)
 
     def filter_columns_by_range(
-            self,
-            filters: zip = None,
-            columns: list[str] = None,
-            upper_bounds: list[float | int] = None,
-            lower_bounds: list[float | int] = None,
+        self,
+        filters: zip = None,
+        columns: list[str] = None,
+        upper_bounds: list[float | int] = None,
+        lower_bounds: list[float | int] = None,
     ):
         """
         Filters columns of the dataset based on specified upper and lower bounds.
@@ -371,6 +371,7 @@ def filter_columns_by_range(
         --------
         remove_non_positive_samples : Method to remove rows with non-positive values for specific parameters.
         """
+
         def apply_bounds(profile, column, upper_bound, lower_bound):
             if upper_bound is not None:
                 profile = profile.filter(pl.col(column) <= upper_bound)
@@ -379,27 +380,31 @@ def apply_bounds(profile, column, upper_bound, lower_bound):
             return profile
 
         for profile_id in (
-                self._data.select(PROFILE_ID_LABEL)
-                        .unique(keep="first")
-                        .to_series()
-                        .to_list()
+            self._data.select(PROFILE_ID_LABEL)
+            .unique(keep="first")
+            .to_series()
+            .to_list()
         ):
             profile = self._data.filter(pl.col(PROFILE_ID_LABEL) == profile_id)
 
             if filters:
                 for column, upper_bound, lower_bound in filters:
                     if column in profile.columns:
-                        profile = apply_bounds(profile, column, upper_bound, lower_bound)
+                        profile = apply_bounds(
+                            profile, column, upper_bound, lower_bound
+                        )
             elif columns and upper_bounds and lower_bounds:
-                for column, upper_bound, lower_bound in zip(columns, upper_bounds, lower_bounds):
+                for column, upper_bound, lower_bound in zip(
+                    columns, upper_bounds, lower_bounds
+                ):
                     profile = apply_bounds(profile, column, upper_bound, lower_bound)
 
-            self._data = self._data.filter(pl.col(PROFILE_ID_LABEL) != profile_id).vstack(profile)
+            self._data = self._data.filter(
+                pl.col(PROFILE_ID_LABEL) != profile_id
+            ).vstack(profile)
 
         self._is_empty(CTD.filter_columns_by_range.__name__)
 
-
-
     def remove_non_positive_samples(self) -> None:
         r"""
         Removes rows with non-positive values for depth, pressure, practical salinity, absolute salinity, or density.
@@ -1196,7 +1201,9 @@ def add_haline_contraction_coefficient(self) -> None:
 
         self._is_empty(CTD.add_haline_contraction_coefficient.__name__)
 
-    def add_mld(self, reference: int, method: str = "potential_density_avg", delta: float = 0.05):
+    def add_mld(
+        self, reference: int, method: str = "potential_density_avg", delta: float = 0.05
+    ):
         r"""
         Calculates and adds the mixed layer depth (MLD) using the density threshold method.