Merge pull request #676 from British-Oceanographic-Data-Centre/675_scipy_integrate_cumtrapz_update

- 675 scipy integrate cumtrapz update
- Updated config files (setup.py and environment.yml) to install dependencies using conda commands.
- Added specific versions to dependencies in config files.
- Replaced pip install command for conda install command in workflows config files.
- Fixed some unit tests.

Author: MagdaJuarez

.github/workflows/build_package.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        python-version: [ '3.9', '3.10' ]
 
     steps:
       - uses: actions/checkout@v4
@@ -21,7 +21,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip virtualenv
-          python -m pip install -r requirements.txt
+          CONDA_BASE=$(conda info --base)
+          source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda env update --prune --file environment.yml 
+          conda activate coast
       - name: Shell Script Permissions
         run: |
           chmod +x *.sh
@@ -33,7 +36,7 @@ jobs:
           ./build.sh
       - name: Test Package Install
         run: |
-          python -m pip install dist/COAsT-*.tar.gz
+          python -m pip install dist/coast-*.tar.gz
       - name: Generate Conda Metadata
         run: |
           ./generate_conda_meta.sh

.github/workflows/markdown-altimetry.yml

@@ -18,10 +18,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: ${{ github.head_ref }}
           path: external
 
-      - name: Prepare environement
+      - name: Prepare environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: coast

.github/workflows/markdown-general.yml

@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: ${{ github.head_ref }}
           path: external
 
       - name: Prepare environment

.github/workflows/markdown-gridded.yml

@@ -18,10 +18,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: ${{ github.head_ref }}
           path: external
 
-      - name: Prepare environement
+      - name: Prepare environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: coast

.github/workflows/markdown-profile.yml

@@ -18,10 +18,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: ${{ github.head_ref }}
           path: external
 
-      - name: Prepare environement
+      - name: Prepare environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: coast

.github/workflows/markdown-tidegauge.yml

@@ -18,10 +18,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: ${{ github.head_ref }}
           path: external
 
-      - name: Prepare environement
+      - name: Prepare environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: coast

.github/workflows/verify_package.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        python-version: [ '3.9', '3.10' ]
 
     steps:
       - uses: actions/checkout@v4
@@ -19,7 +19,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          CONDA_BASE=$(conda info --base)
+          source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda env update --prune --file environment.yml 
+          conda activate coast
       - name: Lint with flake8
         run: |
           pip install flake8
@@ -29,10 +32,10 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pip install dask[complete]
-          pip install -r requirements.txt
+          CONDA_BASE=$(conda info --base)
+          source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda env update --prune --file environment.yml 
+          conda activate coast
           sudo apt-get update
           sudo apt-get install -y libgeos-dev
-          pip install cartopy==0.21.0
-          pip install zarr
           pytest tests

coast/_utils/docsy_tools.py

@@ -1,4 +1,5 @@
 """A class to help with writting markdown."""
+
 from typing import List, Type
 
 

coast/_utils/general_utils.py

@@ -1,4 +1,5 @@
 """A general utility file."""
+
 import xarray as xr
 import numpy as np
 import sklearn.neighbors as nb

coast/_utils/logging_util.py

@@ -1,4 +1,5 @@
 """A logging unilty file"""
+
 import logging
 import sys
 import io