Fix CI - Failing due to missing hdf5 and netcdf headers (#92)

Author: btschwertfeger

.github/workflows/_build.yaml

@@ -37,6 +37,10 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install build
 
+      - name: Install hdf5 and netcdf (macOS)
+        if: runner.os == 'macOS'
+        run: brew install hdf5 netcdf
+
       - name: Check git status (not Windows)
         if: runner.os != 'Windows'
         run: |

.pre-commit-config.yaml

@@ -1,25 +1,15 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.4.2
     hooks:
       - id: ruff
-        args:
-          - --preview
-          - --fix
-          - --exit-non-zero-on-fix
+        args: [--fix]
+      - id: ruff-format
   - repo: https://github.com/pycqa/flake8
     rev: 7.0.0
     hooks:
       - id: flake8
         args: ["--select=E9,F63,F7,F82", "--show-source", "--statistics"]
-  - repo: https://github.com/pycqa/pylint
-    rev: v3.0.3
-    hooks:
-      - id: pylint
-        name: pylint
-        types: [python]
-        exclude: ^examples/|^tests/|^setup.py$
-        args: ["--rcfile=pyproject.toml"]
   # - repo: https://github.com/pre-commit/mirrors-mypy # FIXME
   #   rev: v1.8.0
   #   hooks:
@@ -67,16 +57,16 @@ repos:
       # - id: rst-inline-touching-normal
       - id: rst-directive-colons
       - id: text-unicode-replacement-char
-  - repo: https://github.com/psf/black
-    rev: 24.2.0
-    hooks:
-      - id: black
+  # - repo: https://github.com/psf/black
+  #   rev: 24.2.0
+  #   hooks:
+  #     - id: black
   # - repo: https://github.com/adamchainz/blacken-docs
   #   rev: 1.16.0
   #   hooks:
   #     - id: blacken-docs
   #       additional_dependencies: [black==23.12.0]
-  - repo: https://github.com/PyCQA/isort
+  - repo: https://github.com/PyCQA/isort # TODO: remove as soon as ruff is stable
     rev: 5.13.2
     hooks:
       - id: isort

CHANGELOG.md

@@ -2,20 +2,60 @@
 
 ## [Unreleased](https://github.com/btschwertfeger/python-cmethods/tree/HEAD)
 
-[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.0.2...HEAD)
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.2.1...HEAD)
 
 **Merged pull requests:**
 
-- Fix typos and update pre-commit hooks [\#64](https://github.com/btschwertfeger/python-cmethods/pull/64) ([btschwertfeger](https://github.com/btschwertfeger))
+- Bump actions/checkout from 4.1.2 to 4.1.4 [\#90](https://github.com/btschwertfeger/python-cmethods/pull/90) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump actions/upload-artifact from 4.3.1 to 4.3.2 [\#89](https://github.com/btschwertfeger/python-cmethods/pull/89) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump codecov/codecov-action from 4.2.0 to 4.3.0 [\#87](https://github.com/btschwertfeger/python-cmethods/pull/87) ([dependabot[bot]](https://github.com/apps/dependabot))
+
+## [v2.2.1](https://github.com/btschwertfeger/python-cmethods/tree/v2.2.1) (2024-04-10)
+
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.2.0...v2.2.1)
+
+**Merged pull requests:**
+
+- Fix missing function documentation [\#85](https://github.com/btschwertfeger/python-cmethods/pull/85) ([btschwertfeger](https://github.com/btschwertfeger))
+
+## [v2.2.0](https://github.com/btschwertfeger/python-cmethods/tree/v2.2.0) (2024-04-09)
+
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.1.0...v2.2.0)
+
+**Implemented enhancements:**
+
+- Add a command-line interface [\#82](https://github.com/btschwertfeger/python-cmethods/issues/82)
+- Resolve "Add a command-line interface" [\#83](https://github.com/btschwertfeger/python-cmethods/pull/83) ([btschwertfeger](https://github.com/btschwertfeger))
+
+**Merged pull requests:**
+
+- Bump codecov/codecov-action from 4.1.0 to 4.2.0 [\#80](https://github.com/btschwertfeger/python-cmethods/pull/80) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump actions/setup-python from 5.0.0 to 5.1.0 [\#79](https://github.com/btschwertfeger/python-cmethods/pull/79) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Adjust GitHub Action permissions [\#75](https://github.com/btschwertfeger/python-cmethods/pull/75) ([btschwertfeger](https://github.com/btschwertfeger))
+- Bump actions/upload-artifact from 3.1.0 to 4.3.1 [\#74](https://github.com/btschwertfeger/python-cmethods/pull/74) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump actions/checkout from 3.1.0 to 4.1.2 [\#72](https://github.com/btschwertfeger/python-cmethods/pull/72) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Bump ossf/scorecard-action from 2.1.2 to 2.3.1 [\#71](https://github.com/btschwertfeger/python-cmethods/pull/71) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Update the documentation + project maintenance [\#70](https://github.com/btschwertfeger/python-cmethods/pull/70) ([btschwertfeger](https://github.com/btschwertfeger))
+- Add `scorecard.yml` workflow [\#69](https://github.com/btschwertfeger/python-cmethods/pull/69) ([btschwertfeger](https://github.com/btschwertfeger))
+
+## [v2.1.0](https://github.com/btschwertfeger/python-cmethods/tree/v2.1.0) (2024-03-10)
+
+[Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.0.2...v2.1.0)
+
+**Implemented enhancements:**
+
+- Adjustments using `adjust` require the input data of the control period to have the same size for the time dimension [\#66](https://github.com/btschwertfeger/python-cmethods/issues/66)
+- Resolve "Adjustments using `adjust` require the input data of the control period to have the same size for the time dimension" [\#67](https://github.com/btschwertfeger/python-cmethods/pull/67) ([btschwertfeger](https://github.com/btschwertfeger))
 
 ## [v2.0.2](https://github.com/btschwertfeger/python-cmethods/tree/v2.0.2) (2024-02-02)
 
 [Full Changelog](https://github.com/btschwertfeger/python-cmethods/compare/v2.0.1...v2.0.2)
 
 **Merged pull requests:**
 
-- Update documentation -- QM and QDM formulas [\#62](https://github.com/btschwertfeger/python-cmethods/pull/62) ([btschwertfeger](https://github.com/btschwertfeger))
 - Bump GitHub action versions [\#59](https://github.com/btschwertfeger/python-cmethods/pull/59) ([btschwertfeger](https://github.com/btschwertfeger))
+- Fix typos and update pre-commit hooks [\#64](https://github.com/btschwertfeger/python-cmethods/pull/64) ([btschwertfeger](https://github.com/btschwertfeger))
+- Update documentation -- QM and QDM formulas [\#62](https://github.com/btschwertfeger/python-cmethods/pull/62) ([btschwertfeger](https://github.com/btschwertfeger))
 
 ## [v2.0.1](https://github.com/btschwertfeger/python-cmethods/tree/v2.0.1) (2024-02-01)
 

Makefile

@@ -8,6 +8,7 @@ VENV := venv
 PYTHON := $(VENV)/bin/python3
 TESTS := tests
 PYTEST_OPTS := -vv
+ROOT_DIR:=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))
 
 .PHONY: help
 help:
@@ -75,13 +76,14 @@ ruff:
 .PHONY: ruff-fix
 ruff-fix:
 	ruff check --fix --preview .
+	ruff format .
 
 ## changelog		Create the changelog
 ##
 .PHONY: changelog
 changelog:
 	docker run -it --rm \
-		-v "$(PWD)":/usr/local/src/your-app/ \
+		-v $(ROOT_DIR):/usr/local/src/your-app/ \
 		githubchangeloggenerator/github-changelog-generator \
 		-u btschwertfeger \
 		-p python-cmethods \
@@ -104,6 +106,3 @@ clean:
 	find tests -name "__pycache__" | xargs rm -rf
 	find cmethods -name "__pycache__" | xargs rm -rf
 	find examples -name "__pycache__" | xargs rm -rf
-
-# for file in `ls .github/workflows`; do sed -i '' 's/actions\/checkout@v4/actions\/checkout@1e31de5234b9f8995739874a8ce0492dc87873e2  # v4.0.0/g' .github/workflows/$file; done
-# for file in `ls .github/workflows`; do sed -i '' 's/actions\/setup-python@v5/actions\/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c  # v5.0.0/g' .github/workflows/$file; done

README.md

@@ -137,6 +137,9 @@ https://python-cmethods.readthedocs.io/en/stable/
 
 ## 3. Installation
 
+> For optimal compatibility on macOS, ensure that 'hdf5' and 'netcdf' are
+> pre-installed using Homebrew (`brew install hdf5 netcdf`).
+
 ```bash
 python3 -m pip install python-cmethods
 ```

cmethods/__init__.py

@@ -6,23 +6,23 @@
 # pylint: disable=consider-using-f-string,logging-not-lazy
 
 r"""
-    Module providing the a method named "adjust" to apply different bias
-    correction techniques to time-series climate data.
-
-    Some variables used in this package:
-
-    T = Temperatures ($T$)
-    X = Some climate variable ($X$)
-    h = historical
-    p = scenario; future; predicted
-    obs = observed data ($T_{obs,h}$)
-    simh = modeled data with same time period as obs ($T_{sim,h}$)
-    simp = data to correct (predicted simulated data) ($T_{sim,p}$)
-    F = Cumulative Distribution Function
-    \mu = mean
-    \sigma = standard deviation
-    i = index
-    _{m} = long-term monthly interval
+Module providing the a method named "adjust" to apply different bias
+correction techniques to time-series climate data.
+
+Some variables used in this package:
+
+T = Temperatures ($T$)
+X = Some climate variable ($X$)
+h = historical
+p = scenario; future; predicted
+obs = observed data ($T_{obs,h}$)
+simh = modeled data with same time period as obs ($T_{sim,h}$)
+simp = data to correct (predicted simulated data) ($T_{sim,p}$)
+F = Cumulative Distribution Function
+\mu = mean
+\sigma = standard deviation
+i = index
+_{m} = long-term monthly interval
 """
 
 from __future__ import annotations
@@ -128,9 +128,7 @@
         help="Temporal grouping",
     ),
     constraint=If(
-        Equal("method", "linear_scaling")
-        & Equal("method", "variance_scaling")
-        & Equal("method", "delta_method"),
+        Equal("method", "linear_scaling") & Equal("method", "variance_scaling") & Equal("method", "delta_method"),
         then=require_all,
     ),
 )

cmethods/core.py

@@ -57,8 +57,7 @@ def apply_ufunc(
             not isinstance(value, str) for value in kwargs["input_core_dims"].values()
         ):
             raise ValueError(
-                "input_core_dims must have three key-value pairs like: "
-                '{"obs": "time", "simh": "time", "simp": "time"}',
+                'input_core_dims must have three key-value pairs like: {"obs": "time", "simh": "time", "simp": "time"}',
             )
 
         input_core_dims = kwargs["input_core_dims"]
@@ -187,9 +186,7 @@ def adjust(
             **kwargs,
         )
 
-        result = (
-            monthly_result if result is None else xr.merge([result, monthly_result])
-        )
+        result = monthly_result if result is None else xr.merge([result, monthly_result])
 
     return result
 

cmethods/distribution.py

@@ -159,9 +159,7 @@ def detrended_quantile_mapping(
                 xbins,
                 cdf_simh,
             )  # Eq. 1
-            X = (
-                get_inverse_of_cdf(cdf_obs, epsilon, xbins) + m_simp_mean - m_simh_mean
-            )  # Eq. 1
+            X = get_inverse_of_cdf(cdf_obs, epsilon, xbins) + m_simp_mean - m_simh_mean  # Eq. 1
 
         else:  # kind in cls.MULTIPLICATIVE:
             epsilon = np.interp(  # Eq. 2

cmethods/utils.py

@@ -32,7 +32,7 @@ def __init__(self: UnknownMethodError, method: str, available_methods: list):
 
 def check_adjust_called(
     function_name: str,
-    adjust_called: Optional[bool] = None,  # noqa: FBT001
+    adjust_called: Optional[bool] = None,
 ) -> None:
     """
     Displays a user warning in case a correction function was not called via
@@ -55,9 +55,7 @@ def check_xr_types(obs: XRData, simh: XRData, simp: XRData) -> None:
     """
     Checks if the parameters are in the correct type. **only used internally**
     """
-    phrase: str = (
-        "must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray"
-    )
+    phrase: str = "must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray"
 
     if not isinstance(obs, XRData_t):
         raise TypeError(f"'obs' {phrase}")

doc/getting_started.rst

@@ -9,6 +9,9 @@ Getting Started
 Installation
 ------------
 
+(For optimal compatibility on macOS, ensure that 'hdf5' and 'netcdf' are
+pre-installed using Homebrew (``brew install hdf5 netcdf``).)
+
 The `python-cmethods`_ module can be installed using the package manager pip:
 
 .. code-block:: bash