From 6acd4cefa281e46cedcc400a1858d88e6f686edb Mon Sep 17 00:00:00 2001
From: Sandor Kertesz <Sandor.Kertesz@ecmwf.int>
Date: Fri, 26 Apr 2024 14:01:47 +0100
Subject: [PATCH 1/4] Add tests for solar module

---
 tests/solar/test_solar.py | 53 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/tests/solar/test_solar.py b/tests/solar/test_solar.py
index 0959128..bb362b8 100644
--- a/tests/solar/test_solar.py
+++ b/tests/solar/test_solar.py
@@ -25,3 +25,56 @@
 def test_julian_day(date, expected_value):
     v = solar.julian_day(date)
     assert np.isclose(v, expected_value)
+
+
+@pytest.mark.parametrize(
+    "date,expected_value",
+    [
+        (datetime.datetime(2024, 4, 22), (12.235799080498582, 0.40707190497656276)),
+        (
+            datetime.datetime(2024, 4, 22, 12, 0, 0),
+            (12.403019177270453, 0.43253901867797273),
+        ),
+    ],
+)
+def test_solar_declination_angle(date, expected_value):
+    declination, time_correction = solar.solar_declination_angle(date)
+    assert np.isclose(declination, expected_value[0])
+    assert np.isclose(time_correction, expected_value[1])
+
+
+def test_cos_solar_zenith_angle():
+    date = datetime.datetime(2024, 4, 22, 12, 0, 0)
+    latitudes = np.array([40.0])
+    longitudes = np.array([18.0])
+
+    v = solar.cos_solar_zenith_angle(date, latitudes, longitudes)
+    assert np.isclose(v[0], 0.8478445449796352)
+
+
+def test_cos_solar_zenith_angle_integrated():
+    begin_date = datetime.datetime(2024, 4, 22)
+    end_date = datetime.datetime(2024, 4, 23)
+    latitudes = np.array([40.0])
+    longitudes = np.array([18.0])
+
+    v = solar.cos_solar_zenith_angle_integrated(
+        begin_date, end_date, latitudes, longitudes
+    )
+    assert np.isclose(v[0], 0.3110738757)
+
+
+def test_incoming_solar_radiation():
+    date = datetime.datetime(2024, 4, 22, 12, 0, 0)
+    v = solar.incoming_solar_radiation(date)
+    assert np.isclose(v, 4833557.3088814365)
+
+
+def test_toa_incident_solar_radiation():
+    begin_date = datetime.datetime(2024, 4, 22)
+    end_date = datetime.datetime(2024, 4, 23)
+    latitudes = np.array([40.0])
+    longitudes = np.array([18.0])
+
+    v = solar.toa_incident_solar_radiation(begin_date, end_date, latitudes, longitudes)
+    assert np.isclose(v, 1503617.8237746414)

From f753676e3845e3bb75dc8d96773a24603746ea3b Mon Sep 17 00:00:00 2001
From: Sandor Kertesz <Sandor.Kertesz@ecmwf.int>
Date: Wed, 8 May 2024 15:25:26 +0100
Subject: [PATCH 2/4] Use pyproject.toml and src root dir (#14)

* Use pyproject.toml and src root dir
---
 .github/workflows/cd-pypi.yml                 |  11 ++
 .github/workflows/legacy-ci.yml               | 129 +-----------------
 .gitignore                                    |   1 +
 docs/conf.py                                  |   4 +-
 pyproject.toml                                |  53 ++++++-
 setup.cfg                                     |  36 -----
 {earthkit => src/earthkit}/meteo/__init__.py  |   2 +-
 .../earthkit}/meteo/constants/__init__.py     |   0
 .../earthkit}/meteo/constants/constants.py    |   0
 .../earthkit}/meteo/extreme/__init__.py       |   0
 .../earthkit}/meteo/extreme/array/__init__.py |   0
 .../earthkit}/meteo/extreme/array/cpf.py      |   0
 .../earthkit}/meteo/extreme/array/efi.py      |   0
 .../earthkit}/meteo/extreme/array/sot.py      |   0
 .../earthkit}/meteo/extreme/cpf.py            |   0
 .../earthkit}/meteo/extreme/efi.py            |   0
 .../earthkit}/meteo/extreme/sot.py            |   0
 .../earthkit}/meteo/score/__init__.py         |   0
 .../earthkit}/meteo/score/array/__init__.py   |   0
 .../earthkit}/meteo/score/array/crps.py       |   0
 .../earthkit}/meteo/score/crps.py             |   0
 .../earthkit}/meteo/solar/__init__.py         |   0
 .../earthkit}/meteo/solar/array/__init__.py   |   0
 .../earthkit}/meteo/solar/array/solar.py      |   0
 .../earthkit}/meteo/solar/solar.py            |   0
 .../earthkit}/meteo/stats/__init__.py         |   0
 .../earthkit}/meteo/stats/array/__init__.py   |   0
 .../meteo/stats/array/numpy_extended.py       |   0
 .../earthkit}/meteo/stats/array/quantiles.py  |   0
 .../earthkit}/meteo/stats/numpy_extended.py   |   0
 .../earthkit}/meteo/stats/quantiles.py        |   0
 .../earthkit}/meteo/thermo/__init__.py        |   0
 .../earthkit}/meteo/thermo/array/__init__.py  |   0
 .../earthkit}/meteo/thermo/array/thermo.py    |   0
 .../earthkit}/meteo/thermo/thermo.py          |   0
 .../earthkit}/meteo/wind/__init__.py          |   0
 .../earthkit}/meteo/wind/array/__init__.py    |   0
 .../earthkit}/meteo/wind/array/wind.py        |   0
 {earthkit => src/earthkit}/meteo/wind/wind.py |   0
 39 files changed, 62 insertions(+), 174 deletions(-)
 create mode 100644 .github/workflows/cd-pypi.yml
 rename {earthkit => src/earthkit}/meteo/__init__.py (94%)
 rename {earthkit => src/earthkit}/meteo/constants/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/constants/constants.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/array/cpf.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/array/efi.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/array/sot.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/cpf.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/efi.py (100%)
 rename {earthkit => src/earthkit}/meteo/extreme/sot.py (100%)
 rename {earthkit => src/earthkit}/meteo/score/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/score/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/score/array/crps.py (100%)
 rename {earthkit => src/earthkit}/meteo/score/crps.py (100%)
 rename {earthkit => src/earthkit}/meteo/solar/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/solar/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/solar/array/solar.py (100%)
 rename {earthkit => src/earthkit}/meteo/solar/solar.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/array/numpy_extended.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/array/quantiles.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/numpy_extended.py (100%)
 rename {earthkit => src/earthkit}/meteo/stats/quantiles.py (100%)
 rename {earthkit => src/earthkit}/meteo/thermo/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/thermo/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/thermo/array/thermo.py (100%)
 rename {earthkit => src/earthkit}/meteo/thermo/thermo.py (100%)
 rename {earthkit => src/earthkit}/meteo/wind/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/wind/array/__init__.py (100%)
 rename {earthkit => src/earthkit}/meteo/wind/array/wind.py (100%)
 rename {earthkit => src/earthkit}/meteo/wind/wind.py (100%)

diff --git a/.github/workflows/cd-pypi.yml b/.github/workflows/cd-pypi.yml
new file mode 100644
index 0000000..6104026
--- /dev/null
+++ b/.github/workflows/cd-pypi.yml
@@ -0,0 +1,11 @@
+name: cd
+
+on:
+  push:
+    tags:
+    - '**'
+
+jobs:
+  pypi:
+    uses: ecmwf-actions/reusable-workflows/.github/workflows/cd-pypi.yml@v2
+    secrets: inherit
diff --git a/.github/workflows/legacy-ci.yml b/.github/workflows/legacy-ci.yml
index 921fb15..b9619d8 100644
--- a/.github/workflows/legacy-ci.yml
+++ b/.github/workflows/legacy-ci.yml
@@ -36,62 +36,7 @@ jobs:
         python-version: 3.x
     - uses: pre-commit/action@v3.0.0
 
-  unit-tests:
-    name: unit-tests (3.10)
-    if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.event.pull_request.head.sha || github.ref }}
-    - name: Install Conda environment with Micromamba
-      uses: mamba-org/provision-with-micromamba@v14
-      with:
-        environment-file: tests/environment-unit-tests.yml
-        environment-name: DEVELOP
-        channels: conda-forge
-        cache-env: true
-        extra-specs: |
-          python=3.10
-    - name: Install package
-      run: |
-        python -m pip install --no-deps -e .
-    - name: Run tests
-      run: |
-        make unit-tests
-
-  type-check:
-    needs: [unit-tests]
-    if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.event.pull_request.head.sha || github.ref }}
-    - name: Install Conda environment with Micromamba
-      uses: mamba-org/provision-with-micromamba@v12
-      with:
-        environment-file: environment.yml
-        environment-name: DEVELOP
-        channels: conda-forge
-        cache-env: true
-        cache-env-key: ubuntu-latest-3.10
-        extra-specs: |
-          python=3.10
-    - name: Install package
-      run: |
-        python -m pip install --no-deps -e .
-    - name: Run code quality checks
-      run: |
-        echo type-check not used
-
   documentation:
-    needs: [unit-tests]
     if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
     runs-on: ubuntu-latest
     defaults:
@@ -105,7 +50,7 @@ jobs:
     - name: Install Conda environment with Micromamba
       uses: mamba-org/provision-with-micromamba@v12
       with:
-        environment-file: environment.yml
+        environment-file: tests/environment-unit-tests.yml
         environment-name: DEVELOP
         channels: conda-forge
         cache-env: true
@@ -118,75 +63,3 @@ jobs:
     - name: Build documentation
       run: |
         make docs-build
-
-  integration-tests:
-    needs: [unit-tests]
-    if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-
-    strategy:
-      matrix:
-        include:
-        - python-version: "3.10"
-              # extra: -minver  # This will need to be uncommented and environment-minver.yml updated if we want to publish on conda
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.event.pull_request.head.sha || github.ref }}
-    - name: Install Conda environment with Micromamba
-      uses: mamba-org/provision-with-micromamba@v12
-      with:
-        environment-file: tests/environment-unit-tests${{ matrix.extra }}.yml
-        environment-name: DEVELOP${{ matrix.extra }}
-        channels: conda-forge
-        cache-env: true
-        cache-env-key: ubuntu-latest-${{ matrix.python-version }}${{ matrix.extra }}.
-        extra-specs: |
-          python=${{matrix.python-version }}
-    - name: Install package
-      run: |
-        python -m pip install --no-deps -e .
-    - name: Run tests
-      run: |
-        make unit-tests
-
-  distribution:
-    needs: [integration-tests, type-check, documentation]
-    if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.event.pull_request.head.sha || github.ref }}
-    - name: Build distributions
-      run: |
-        $CONDA/bin/python -m pip install build
-        $CONDA/bin/python -m build
-    - name: Publish a Python distribution to PyPI
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-
-  notify:
-    if: always() && ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
-    needs:
-    - pre-commit
-    - unit-tests
-    - type-check
-    - documentation
-    - integration-tests
-    - distribution
-    runs-on: ubuntu-latest
-    steps:
-    - name: Trigger Teams notification
-      uses: ecmwf-actions/notify-teams@v1
-      with:
-        incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}
-        needs_context: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
index 913eabb..e46c00f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 # setuptools-scm
 version.py
+_version.py
 
 # Sphinx automatic generation of API
 docs/_api/
diff --git a/docs/conf.py b/docs/conf.py
index d34cfb9..4854c59 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -42,8 +42,8 @@
 autodoc_typehints = "none"
 
 # autoapi configuration
-autoapi_dirs = ["../earthkit/meteo"]
-autoapi_ignore = ["*/version.py", "sphinxext/*"]
+autoapi_dirs = ["../src/earthkit/meteo"]
+autoapi_ignore = ["*/_version.py", "sphinxext/*"]
 autoapi_options = [
     "members",
     "undoc-members",
diff --git a/pyproject.toml b/pyproject.toml
index 1441605..7279832 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,47 @@
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=61", "setuptools-scm>=8.0"]
+
+[project]
+authors = [
+  {name = "European Centre for Medium-Range Weather Forecasts (ECMWF)", email = "software.support@ecmwf.int"}
+]
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+  "Operating System :: OS Independent"
+]
+dependencies = [
+  "numpy"
+]
+description = "Meteorological computations"
+dynamic = ["version"]
+license = {text = "Apache License Version 2.0"}
+name = "earthkit-meteo"
+readme = "README.md"
+requires-python = ">= 3.8"
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+  "pytest-cov"
+]
+
+[project.urls]
+Documentation = "https://earthkit-meteo.readthedocs.io/"
+Homepage = "https://github.com/ecmwf/earthkit-meteo/"
+Issues = "https://github.com/ecmwf/earthkit-meteo.issues"
+Repository = "https://github.com/ecmwf/earthkit-meteo/"
 
 [tool.coverage.run]
-branch = true
+branch = "true"
 
 [tool.isort]
 profile = "black"
@@ -11,9 +50,9 @@ profile = "black"
 add_ignore = ["D1", "D200", "D205", "D400", "D401"]
 convention = "numpy"
 
+[tool.setuptools.packages.find]
+include = ["earthkit.meteo"]
+where = ["src/"]
+
 [tool.setuptools_scm]
-write_to = "earthkit/meteo/version.py"
-write_to_template = '''
-# Do not change! Do not track in version control!
-__version__ = "{version}"
-'''
+version_file = "src/earthkit/meteo/_version.py"
diff --git a/setup.cfg b/setup.cfg
index 6e27fe8..4736e11 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,39 +1,3 @@
-[metadata]
-name = earthkit-meteo
-license = Apache License 2.0
-description = Meteorological computations
-    Development Status :: 2 - Pre-Alpha
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: Apache Software License
-    Operating System :: OS Independent
-    Programming Language :: Python
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    Topic :: Scientific/Engineering
-long_description_content_type=text/markdown
-long_description = file: README.md
-test_suite = tests
-
-[options]
-packages = find_namespace:
-install_requires =
-    numpy
-
-[options.packages.find]
-include = earthkit.*
-
-[options.extras_require]
-test =
-    pytest
-    pytest-cov
-
 [flake8]
 max-line-length = 110
 extend-ignore = E203, W503
-
-[mypy]
-strict = False
-ignore_missing_imports = True
diff --git a/earthkit/meteo/__init__.py b/src/earthkit/meteo/__init__.py
similarity index 94%
rename from earthkit/meteo/__init__.py
rename to src/earthkit/meteo/__init__.py
index d64217c..90d22f3 100644
--- a/earthkit/meteo/__init__.py
+++ b/src/earthkit/meteo/__init__.py
@@ -10,7 +10,7 @@
 try:
     # NOTE: the `version.py` file must not be present in the git repository
     #   as it is generated by setuptools at install time
-    from .version import __version__
+    from ._version import __version__
 except ImportError:  # pragma: no cover
     # Local copy or not installed with setuptools
     __version__ = "999"
diff --git a/earthkit/meteo/constants/__init__.py b/src/earthkit/meteo/constants/__init__.py
similarity index 100%
rename from earthkit/meteo/constants/__init__.py
rename to src/earthkit/meteo/constants/__init__.py
diff --git a/earthkit/meteo/constants/constants.py b/src/earthkit/meteo/constants/constants.py
similarity index 100%
rename from earthkit/meteo/constants/constants.py
rename to src/earthkit/meteo/constants/constants.py
diff --git a/earthkit/meteo/extreme/__init__.py b/src/earthkit/meteo/extreme/__init__.py
similarity index 100%
rename from earthkit/meteo/extreme/__init__.py
rename to src/earthkit/meteo/extreme/__init__.py
diff --git a/earthkit/meteo/extreme/array/__init__.py b/src/earthkit/meteo/extreme/array/__init__.py
similarity index 100%
rename from earthkit/meteo/extreme/array/__init__.py
rename to src/earthkit/meteo/extreme/array/__init__.py
diff --git a/earthkit/meteo/extreme/array/cpf.py b/src/earthkit/meteo/extreme/array/cpf.py
similarity index 100%
rename from earthkit/meteo/extreme/array/cpf.py
rename to src/earthkit/meteo/extreme/array/cpf.py
diff --git a/earthkit/meteo/extreme/array/efi.py b/src/earthkit/meteo/extreme/array/efi.py
similarity index 100%
rename from earthkit/meteo/extreme/array/efi.py
rename to src/earthkit/meteo/extreme/array/efi.py
diff --git a/earthkit/meteo/extreme/array/sot.py b/src/earthkit/meteo/extreme/array/sot.py
similarity index 100%
rename from earthkit/meteo/extreme/array/sot.py
rename to src/earthkit/meteo/extreme/array/sot.py
diff --git a/earthkit/meteo/extreme/cpf.py b/src/earthkit/meteo/extreme/cpf.py
similarity index 100%
rename from earthkit/meteo/extreme/cpf.py
rename to src/earthkit/meteo/extreme/cpf.py
diff --git a/earthkit/meteo/extreme/efi.py b/src/earthkit/meteo/extreme/efi.py
similarity index 100%
rename from earthkit/meteo/extreme/efi.py
rename to src/earthkit/meteo/extreme/efi.py
diff --git a/earthkit/meteo/extreme/sot.py b/src/earthkit/meteo/extreme/sot.py
similarity index 100%
rename from earthkit/meteo/extreme/sot.py
rename to src/earthkit/meteo/extreme/sot.py
diff --git a/earthkit/meteo/score/__init__.py b/src/earthkit/meteo/score/__init__.py
similarity index 100%
rename from earthkit/meteo/score/__init__.py
rename to src/earthkit/meteo/score/__init__.py
diff --git a/earthkit/meteo/score/array/__init__.py b/src/earthkit/meteo/score/array/__init__.py
similarity index 100%
rename from earthkit/meteo/score/array/__init__.py
rename to src/earthkit/meteo/score/array/__init__.py
diff --git a/earthkit/meteo/score/array/crps.py b/src/earthkit/meteo/score/array/crps.py
similarity index 100%
rename from earthkit/meteo/score/array/crps.py
rename to src/earthkit/meteo/score/array/crps.py
diff --git a/earthkit/meteo/score/crps.py b/src/earthkit/meteo/score/crps.py
similarity index 100%
rename from earthkit/meteo/score/crps.py
rename to src/earthkit/meteo/score/crps.py
diff --git a/earthkit/meteo/solar/__init__.py b/src/earthkit/meteo/solar/__init__.py
similarity index 100%
rename from earthkit/meteo/solar/__init__.py
rename to src/earthkit/meteo/solar/__init__.py
diff --git a/earthkit/meteo/solar/array/__init__.py b/src/earthkit/meteo/solar/array/__init__.py
similarity index 100%
rename from earthkit/meteo/solar/array/__init__.py
rename to src/earthkit/meteo/solar/array/__init__.py
diff --git a/earthkit/meteo/solar/array/solar.py b/src/earthkit/meteo/solar/array/solar.py
similarity index 100%
rename from earthkit/meteo/solar/array/solar.py
rename to src/earthkit/meteo/solar/array/solar.py
diff --git a/earthkit/meteo/solar/solar.py b/src/earthkit/meteo/solar/solar.py
similarity index 100%
rename from earthkit/meteo/solar/solar.py
rename to src/earthkit/meteo/solar/solar.py
diff --git a/earthkit/meteo/stats/__init__.py b/src/earthkit/meteo/stats/__init__.py
similarity index 100%
rename from earthkit/meteo/stats/__init__.py
rename to src/earthkit/meteo/stats/__init__.py
diff --git a/earthkit/meteo/stats/array/__init__.py b/src/earthkit/meteo/stats/array/__init__.py
similarity index 100%
rename from earthkit/meteo/stats/array/__init__.py
rename to src/earthkit/meteo/stats/array/__init__.py
diff --git a/earthkit/meteo/stats/array/numpy_extended.py b/src/earthkit/meteo/stats/array/numpy_extended.py
similarity index 100%
rename from earthkit/meteo/stats/array/numpy_extended.py
rename to src/earthkit/meteo/stats/array/numpy_extended.py
diff --git a/earthkit/meteo/stats/array/quantiles.py b/src/earthkit/meteo/stats/array/quantiles.py
similarity index 100%
rename from earthkit/meteo/stats/array/quantiles.py
rename to src/earthkit/meteo/stats/array/quantiles.py
diff --git a/earthkit/meteo/stats/numpy_extended.py b/src/earthkit/meteo/stats/numpy_extended.py
similarity index 100%
rename from earthkit/meteo/stats/numpy_extended.py
rename to src/earthkit/meteo/stats/numpy_extended.py
diff --git a/earthkit/meteo/stats/quantiles.py b/src/earthkit/meteo/stats/quantiles.py
similarity index 100%
rename from earthkit/meteo/stats/quantiles.py
rename to src/earthkit/meteo/stats/quantiles.py
diff --git a/earthkit/meteo/thermo/__init__.py b/src/earthkit/meteo/thermo/__init__.py
similarity index 100%
rename from earthkit/meteo/thermo/__init__.py
rename to src/earthkit/meteo/thermo/__init__.py
diff --git a/earthkit/meteo/thermo/array/__init__.py b/src/earthkit/meteo/thermo/array/__init__.py
similarity index 100%
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rename to src/earthkit/meteo/thermo/array/__init__.py
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diff --git a/earthkit/meteo/wind/__init__.py b/src/earthkit/meteo/wind/__init__.py
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rename to src/earthkit/meteo/wind/__init__.py
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similarity index 100%
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rename to src/earthkit/meteo/wind/array/wind.py
diff --git a/earthkit/meteo/wind/wind.py b/src/earthkit/meteo/wind/wind.py
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rename to src/earthkit/meteo/wind/wind.py

From 06234a658f83e37e11bbe5418aa8793bc74fa1c1 Mon Sep 17 00:00:00 2001
From: Jenny Wong <jenny.wong@ecmwf.int>
Date: Fri, 9 Aug 2024 15:29:21 +0000
Subject: [PATCH 3/4] Propagate nans with computing quantiles with
 method=sorted

---
 src/earthkit/meteo/stats/array/quantiles.py |  2 ++
 tests/stats/test_stats.py                   | 13 +++++++++++++
 2 files changed, 15 insertions(+)

diff --git a/src/earthkit/meteo/stats/array/quantiles.py b/src/earthkit/meteo/stats/array/quantiles.py
index 33e1cd6..52efa50 100644
--- a/src/earthkit/meteo/stats/array/quantiles.py
+++ b/src/earthkit/meteo/stats/array/quantiles.py
@@ -59,6 +59,7 @@ def iter_quantiles(
     if method == "sort":
         arr = np.asarray(arr)
         arr.sort(axis=axis)
+        missing = np.isnan(np.min(arr, axis=axis))
 
     for q in qs:
         if method == "numpy":
@@ -74,4 +75,5 @@ def iter_quantiles(
             tmp = arr.take(min(j + 1, m - 1), axis=axis)
             tmp *= x
             quantile += tmp
+            quantile[missing] = np.nan
             yield quantile
diff --git a/tests/stats/test_stats.py b/tests/stats/test_stats.py
index 7709313..ba7aea4 100644
--- a/tests/stats/test_stats.py
+++ b/tests/stats/test_stats.py
@@ -65,3 +65,16 @@ def test_quantiles(method):
             [5, 19, 12, 3, 45, 48, 8, 9, 7],
         ]
     )
+
+
+def test_quantiles_nans():
+    arr = np.random.rand(100, 100, 100)
+    arr.ravel()[np.random.choice(arr.size, 100000, replace=False)] = np.nan
+    qs = [0.0, 0.25, 0.5, 0.75, 1.0]
+    sort = [
+        quantile for quantile in stats.iter_quantiles(arr.copy(), qs, method="sort")
+    ]
+    numpy = [
+        quantile for quantile in stats.iter_quantiles(arr.copy(), qs, method="numpy")
+    ]
+    assert np.all(np.isclose(sort, numpy, equal_nan=True))

From 54f5fcac223562dfe319c4e8dfb530a9d8546ec2 Mon Sep 17 00:00:00 2001
From: Jenny Wong <jenny.wong@ecmwf.int>
Date: Fri, 9 Aug 2024 15:53:25 +0000
Subject: [PATCH 4/4] Review comment to simplify

---
 src/earthkit/meteo/stats/array/quantiles.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/earthkit/meteo/stats/array/quantiles.py b/src/earthkit/meteo/stats/array/quantiles.py
index 52efa50..0f9109a 100644
--- a/src/earthkit/meteo/stats/array/quantiles.py
+++ b/src/earthkit/meteo/stats/array/quantiles.py
@@ -59,7 +59,7 @@ def iter_quantiles(
     if method == "sort":
         arr = np.asarray(arr)
         arr.sort(axis=axis)
-        missing = np.isnan(np.min(arr, axis=axis))
+        missing = np.isnan(arr).any(axis=axis)
 
     for q in qs:
         if method == "numpy":