Merge pull request #70 from ocefpaf/update_numpy

use numpy >=1.20

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    labels:
+      - "Bot"

.github/workflows/publish.yml → .github/workflows/pypi.yml

@@ -2,21 +2,24 @@
 name: Publish to PyPI
 
 on:
+  pull_request:
+  push:
+    branches:
+      - main
   release:
     types:
       - published
 
 jobs:
-
-  pypi-build:
+  packages:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.x
+        python-version: "3.10"
 
     - name: Get tags
       run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
@@ -37,12 +40,13 @@ jobs:
 
     - name: Test wheels
       run: |
-        cd dist && python -m pip install pocean_core*.whl
+        cd dist && python -m pip install *.whl
         python -m twine check *
       shell: bash
 
     - name: Publish a Python distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      if: success() && github.event_name == 'release'
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/tests.yml

@@ -0,0 +1,38 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@v15
+      with:
+        environment-file: false
+
+    - name: Python ${{ matrix.python-version }}
+      shell: bash -l {0}
+      run: >
+        micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
+        && micromamba activate TEST
+        && python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: >
+        micromamba activate TEST
+        && python -m pytest --disable-warnings

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.1.0
+  rev: v4.4.0
   hooks:
     - id: end-of-file-fixer
       files: .*\.*.py
@@ -18,6 +18,6 @@ repos:
         - requirements-dev.txt
 
 - repo: https://github.com/pycqa/flake8
-  rev: 4.0.1
+  rev: 6.0.0
   hooks:
     - id: flake8

pocean/dsg/timeseriesProfile/r.py

@@ -133,7 +133,7 @@ def from_dataframe(cls, df, output, **kwargs):
                 profile[j] = pname
                 row_size[j] = len(pfg)
                 if s_ind is not None:
-                    s_ind[j] = np.asscalar(np.argwhere(station[:] == pfg[axes.station].dropna().iloc[0]))
+                    s_ind[j] = np.argwhere(station[:] == pfg[axes.station].dropna().iloc[0]).item()
 
             # Add back in the z axes that was removed when calculating data_columns
             # and ignore variables that were stored in the profile index

pocean/dsg/utils.py

@@ -72,6 +72,9 @@ def get_geographic_attributes(df, axes=None):
 
     if len(set(coords)) == 1:
         geoclass = Point
+        # The set is to workaround the fact tht pocean
+        # relied in a shapely<2 bug to pass a vector here instead of a point.
+        coords = set(coords)
     elif len(coords) > 2:
         geoclass = Polygon
     else:

pocean/utils.py

@@ -274,7 +274,7 @@ def create_ncvar_from_series(ncd, var_name, dimensions, series, **kwargs):
     elif series.dtype.kind in ['U', 'S'] or series.dtype in [str]:
         # AttributeError: cannot set _FillValue attribute for VLEN or compound variable
         v = ncd.createVariable(var_name, get_dtype(series), dimensions, **kwargs)
-    elif series.dtype == np.object:
+    elif series.dtype == object:
         # Try to downcast to an int and then just take the type of the result
         # If we can't convert to a numeric use a string
         try:

requirements.txt

@@ -1,6 +1,6 @@
 cftime>=1.2.1
-netcdf4
-numpy>=1.15
+netcdf4<1.6.1
+numpy>=1.20
 pandas>=1.0.5
 python-dateutil
 pytz

setup.cfg

@@ -29,8 +29,8 @@ classifiers =
 packages = find:
 install_requires =
     cftime>=1.2.1
-    netcdf4
-    numpy>=1.15
+    netcdf4<1.6.1
+    numpy>=1.20
     pandas>=1.0.5
     python-dateutil
     pytz
@@ -53,8 +53,9 @@ filterwarnings =
 max-line-length = 100
 ignore =
     E265 E501 E221 E203 E201 E124 E202 E241 E251 W293 W291 W504
-    pocean/tests/*.py F403 F405
-    pocean/tests/*.py F403 F405
+per-file-ignores =
+    pocean/tests/*.py: F403 F405
+    pocean/tests/*.py: F403 F405
 exclude =
     docs/
     .git/