Update umamba gha

.github/workflows/deploy-docs.yml

@@ -19,35 +19,31 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v16
+    - name: Setup Micromamba Python
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 --file requirements.txt --file requirements-dev.txt --channel conda-forge
 
-    - name: Build environment
+    - name: Install ctd
       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: |
+      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
+        && 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'
+      if: success() && github.event_name == 'release'
       uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pypi.yml

@@ -9,6 +9,10 @@ on:
     types:
       - published
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   packages:
     runs-on: ubuntu-latest
@@ -22,27 +26,22 @@ jobs:
 
     - name: Get tags
       run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-      shell: bash
 
     - name: Install build tools
       run: |
-        python -m pip install --upgrade pip wheel setuptools setuptools_scm build twine
-
-      shell: bash
+        python -m pip install --upgrade pip build twine
 
     - name: Build binary wheel
       run: python -m build --sdist --wheel . --outdir dist
 
     - name: CheckFiles
       run: |
         ls dist
-      shell: bash
 
     - name: Test wheels
       run: |
-        cd dist && python -m pip install ctd*.whl
+        cd dist && python -m pip install *.whl
         python -m twine check *
-      shell: bash
 
     - name: Publish a Python distribution to PyPI
       if: success() && github.event_name == 'release'

.github/workflows/tests.yml

@@ -10,33 +10,32 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [windows-latest, ubuntu-latest, macos-latest]
       fail-fast: false
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Setup Micromamba
-      uses: mamba-org/provision-with-micromamba@v16
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: false
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
 
-    - name: Python ${{ matrix.python-version }}
+    - name: Install ctd
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=${{ 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
 
     - name: Doctests
       shell: bash -l {0}
       run: |
-        micromamba activate TEST
         python -m pytest -s -rxs --doctest-modules -vv ctd

.pre-commit-config.yaml

@@ -13,33 +13,24 @@ repos:
     - id: file-contents-sorter
       files: requirements-dev.txt
 
-- repo: https://github.com/econchick/interrogate
-  rev: 1.5.0
-  hooks:
-    - id: interrogate
-      exclude: ^(docs|setup.py|tests)
-      args: [--config=pyproject.toml]
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
-  hooks:
-    - id: flake8
-      exclude: docs/source/conf.py
-      args: [--max-line-length=105, --ignore=E203]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      additional_dependencies: [toml]
-      args: ["--profile", "black", "--filter-files"]
-
 - repo: https://github.com/psf/black
   rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
 
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.8
+  hooks:
+    - id: blackdoc
+
+- repo: https://github.com/econchick/interrogate
+  rev: 1.5.0
+  hooks:
+    - id: interrogate
+      exclude: ^(docs|tests)
+      args: [--config=pyproject.toml]
+
 
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.5
@@ -48,14 +39,28 @@ repos:
       args:
         - --ignore-words-list=pres,nd,te,afe,ue,wil,tey,te,ot,fo
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.7.0
-  hooks:
-    - id: pyupgrade
-      args:
-        - --py36-plus
-
 - repo: https://github.com/asottile/add-trailing-comma
   rev: v2.5.1
   hooks:
     - id: add-trailing-comma
+
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.274
+  hooks:
+    - id: ruff
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: 0.12.1
+  hooks:
+    - id: pyproject-fmt
+
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: false
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: []
+    submodules: false

ctd/plotting.py

@@ -29,7 +29,7 @@ def plot_cast(df, secondary_y=False, label=None, ax=None, *args, **kwargs):
 
     y_inverted = False
     if not getattr(ax, "y_inverted", False):
-        setattr(ax, "y_inverted", True)
+        ax.y_inverted = True
         y_inverted = True
 
     if secondary_y:
@@ -40,11 +40,11 @@ def plot_cast(df, secondary_y=False, label=None, ax=None, *args, **kwargs):
 
     if isinstance(df, pd.DataFrame):
         labels = label if label else df.columns
-        for k, (col, series) in enumerate(df.items()):
+        for k, (_col, series) in enumerate(df.items()):
             ax.plot(series, series.index, label=labels[k])
     elif isinstance(df, pd.Series):
         label = label if label else str(df.name)
-        ax.plot(df.values, df.index, label=label, *args, **kwargs)
+        ax.plot(df.values, df.index, *args, label=label, **kwargs)
 
     ax.set_ylabel(ylabel)
     ax.set_xlabel(xlabel)

ctd/processing.py

@@ -62,16 +62,16 @@ def lp_filter(df, sample_rate=24.0, time_constant=0.15):
     >>> import matplotlib.pyplot as plt
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> raw = ctd.from_cnv(data_path.joinpath('CTD-spiked-unfiltered.cnv.bz2'))
-    >>> prc = ctd.from_cnv(data_path.joinpath('CTD-spiked-filtered.cnv.bz2'))
+    >>> raw = ctd.from_cnv(data_path.joinpath("CTD-spiked-unfiltered.cnv.bz2"))
+    >>> prc = ctd.from_cnv(data_path.joinpath("CTD-spiked-filtered.cnv.bz2"))
     >>> kw = {"sample_rate": 24.0, "time_constant": 0.15}
     >>> original = prc.index.values
     >>> unfiltered = raw.index.values
     >>> filtered = raw.lp_filter(**kw).index.values
     >>> fig, ax = plt.subplots()
-    >>> l1, = ax.plot(original, 'k', label='original')
-    >>> l2, = ax.plot(unfiltered, 'r', label='unfiltered')
-    >>> l3, = ax.plot(filtered, 'g', label='filtered')
+    >>> (l1,) = ax.plot(original, "k", label="original")
+    >>> (l2,) = ax.plot(unfiltered, "r", label="unfiltered")
+    >>> (l3,) = ax.plot(filtered, "g", label="filtered")
     >>> leg = ax.legend()
 
     Notes

ctd/read.py

@@ -202,7 +202,7 @@ def from_bl(fname):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> df = ctd.from_bl(str(data_path.joinpath('bl', 'bottletest.bl')))
+    >>> df = ctd.from_bl(str(data_path.joinpath("bl", "bottletest.bl")))
     >>> df._metadata["time_of_reset"]
     datetime.datetime(2018, 6, 25, 20, 8, 55)
 
@@ -231,7 +231,7 @@ def from_btl(fname):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> bottles = ctd.from_btl(data_path.joinpath('btl', 'bottletest.btl'))
+    >>> bottles = ctd.from_btl(data_path.joinpath("btl", "bottletest.btl"))
 
     """
     f = _read_file(fname)
@@ -291,10 +291,13 @@ def from_btl(fname):
             try:
                 df[column] = df[column].astype(float)
             except ValueError:
-                warnings.warn("Could not convert %s to float." % column)
+                warnings.warn(
+                    f"Could not convert {column} to float.",
+                    stacklevel=2,
+                )
 
     df["Date"] = pd.to_datetime(df["Date"])
-    setattr(df, "_metadata", metadata)
+    df._metadata = metadata
     return df
 
 
@@ -307,8 +310,8 @@ def from_edf(fname):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> cast = ctd.from_edf(data_path.joinpath('XBT.EDF.gz'))
-    >>> ax = cast['temperature'].plot_cast()
+    >>> cast = ctd.from_edf(data_path.joinpath("XBT.EDF.gz"))
+    >>> ax = cast["temperature"].plot_cast()
 
     """
     f = _read_file(fname)
@@ -370,7 +373,7 @@ def from_edf(fname):
         "header": "\n".join(header),
         "serial": serial,
     }
-    setattr(df, "_metadata", metadata)
+    df._metadata = metadata
     return df
 
 
@@ -383,9 +386,9 @@ def from_cnv(fname):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> cast = ctd.from_cnv(data_path.joinpath('CTD_big.cnv.bz2'))
+    >>> cast = ctd.from_cnv(data_path.joinpath("CTD_big.cnv.bz2"))
     >>> downcast, upcast = cast.split()
-    >>> ax = downcast['t090C'].plot_cast()
+    >>> ax = downcast["t090C"].plot_cast()
 
     """
     f = _read_file(fname)
@@ -451,10 +454,13 @@ def from_cnv(fname):
             try:
                 df[column] = df[column].astype(float)
             except ValueError:
-                warnings.warn("Could not convert %s to float." % column)
+                warnings.warn(
+                    f"Could not convert {column} to float.",
+                    stacklevel=2,
+                )
 
     metadata["name"] = str(name)
-    setattr(df, "_metadata", metadata)
+    df._metadata = metadata
     return df
 
 
@@ -468,9 +474,9 @@ def from_fsi(fname, skiprows=9):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> cast = ctd.from_fsi(data_path.joinpath('FSI.txt.gz'))
+    >>> cast = ctd.from_fsi(data_path.joinpath("FSI.txt.gz"))
     >>> downcast, upcast = cast.split()
-    >>> ax = downcast['TEMP'].plot_cast()
+    >>> ax = downcast["TEMP"].plot_cast()
 
     """
     f = _read_file(fname)
@@ -487,7 +493,7 @@ def from_fsi(fname, skiprows=9):
     df.set_index("PRES", drop=True, inplace=True)
     df.index.name = "Pressure [dbar]"
     metadata = {"name": str(fname)}
-    setattr(df, "_metadata", metadata)
+    df._metadata = metadata
     return df
 
 
@@ -505,7 +511,7 @@ def rosette_summary(fname):
     >>> from pathlib import Path
     >>> import ctd
     >>> data_path = Path(__file__).parents[1].joinpath("tests", "data")
-    >>> fname = data_path.joinpath('CTD/g01l01s01.ros')
+    >>> fname = data_path.joinpath("CTD/g01l01s01.ros")
     >>> ros = ctd.rosette_summary(fname)
     >>> ros = ros.groupby(ros.index).mean()
     >>> ros.pressure.values.astype(int)
@@ -526,7 +532,7 @@ def from_castaway_csv(fname):
     Example
     --------
     >>> import ctd
-    >>> cast = ctd.from_castaway_csv('tests/data/castaway_data.csv')
+    >>> cast = ctd.from_castaway_csv("tests/data/castaway_data.csv")
     >>> cast.columns
     Index(['depth', 'temperature', 'conductivity', 'specific_conductance',
            'salinity', 'sound_velocity', 'density'],
@@ -561,6 +567,6 @@ def from_castaway_csv(fname):
     for line in meta:
         metadata[line[0]] = line[1]
     metadata["units"] = units
-    setattr(df, "_metadata", metadata)
+    df._metadata = metadata
 
     return df