Update tests

.github/workflows/deploy-docs.yml

@@ -0,0 +1,54 @@
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: false
+
+    - name: Build environment
+      shell: bash -l {0}
+      run: |
+        micromamba create --name TEST python=3 --file requirements.txt --file requirements-dev.txt --channel conda-forge
+        micromamba activate TEST
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Get the version
+      id: get_version
+      run: echo ::set-output name=VERSION::$(python setup.py --version)
+
+    - name: Build documentation
+      shell: bash -l {0}
+      run: |
+        set -e
+        micromamba activate TEST
+        jupyter nbconvert --to notebook --execute notebooks/quick_intro.ipynb --output=quick_intro-output.ipynb
+        mv notebooks/*output.ipynb docs/source/
+        pushd docs
+        make clean html linkcheck
+        popd
+
+    - name: Deploy
+      if: github.event_name == 'release' || github.event_name == 'push'
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

.github/workflows/tests.yml

@@ -0,0 +1,36 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@main
+      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 -rxs tests

.gitignore

@@ -7,3 +7,5 @@
 build/
 ctd/_version.py
 dist/
+*-output.ipynb
+*.pyc

ctd/processing.py

@@ -255,10 +255,8 @@ def movingaverage(df, window_size=48):
     """
     Moving average on a data frame or series.
 
-    Inputs
-    ------
-    windows_size : integer
-        Size of the window.
+    Inputs:
+      windows_size : integer
 
     """
 

docs/source/index.rst

@@ -7,7 +7,7 @@ Load and pre-process CTD/XBT casts as pandas DataFrames.
 .. toctree::
    :maxdepth: 3
 
-   quick_intro.ipynb
+   quick_intro-output.ipynb
    ctd
 
 Indices and tables

notebooks/quick_intro.ipynb

@@ -12,7 +12,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [],
    "source": [
     "import io\n",
@@ -32,7 +34,7 @@
     "        Path(\"CTD-spiked-unfiltered.cnv.bz2\").write_bytes(data.read())\n",
     "\n",
     "\n",
-    "url = \"https://github.com/pyoceans/python-ctd/raw/master/tests/data/CTD-spiked-unfiltered.cnv.bz2\"\n",
+    "url = \"https://github.com/pyoceans/python-ctd/raw/main/tests/data/CTD-spiked-unfiltered.cnv.bz2\"\n",
     "download_demo_file(url)"
    ]
   },
@@ -117,7 +119,7 @@
     "ax1.grid(False)\n",
     "\n",
     "ax0.legend(loc=\"lower left\")\n",
-    "ax1.legend(loc=\"lower right\")"
+    "ax1.legend(loc=\"lower right\");"
    ]
   },
   {
@@ -173,7 +175,7 @@
     "ax.plot(down.index, label=\"unfiltered\")\n",
     "ax.plot(down.lp_filter().index, label=\"filtered\")\n",
     "ax.axis([20870, 20930, 557.5, 559])\n",
-    "fig.legend()"
+    "fig.legend();"
    ]
   },
   {
@@ -234,11 +236,11 @@
     "\n",
     "p = proc.index\n",
     "\n",
-    "SP = gsw.SP_from_C(proc[\"c0S/m\"] * 10.0, proc[\"t090C\"], p)\n",
+    "SP = gsw.SP_from_C(proc[\"c0S/m\"].to_numpy() * 10.0, proc[\"t090C\"].to_numpy(), p)\n",
     "SA = gsw.SA_from_SP(SP, p, lon, lat)\n",
     "SR = gsw.SR_from_SP(SP)\n",
     "\n",
-    "CT = gsw.CT_from_t(SA, proc[\"t090C\"].values, p)\n",
+    "CT = gsw.CT_from_t(SA, proc[\"t090C\"].to_numpy(), p)\n",
     "z = -gsw.z_from_p(p, lat)\n",
     "sigma0_CT = gsw.sigma0(SA, CT)\n",
     "\n",
@@ -272,7 +274,7 @@
     "ax.set_ylabel(\"Pressure (dbar)\")\n",
     "ax.grid(True)\n",
     "ax.legend()\n",
-    "ax.set_title(\"Salinities\")"
+    "ax.set_title(\"Salinities\");"
    ]
   },
   {
@@ -344,7 +346,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -358,7 +360,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,