update dependencies and enable codecov (#454)

* update dependencies * update lock files * enable codecov report * change ci-tests matrix job name * update badge * iris cut'n paste correction
SciTools · Apr 25, 2024 · c43905d · c43905d
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diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -23,7 +23,7 @@ concurrency:
 
 jobs:
   tests:
-    name: "${{ matrix.session }} (py${{ matrix.python-version }} ${{ matrix.os }}) [${{ matrix.iris-source }}]"
+    name: "${{ matrix.session }} py${{ matrix.python-version }} [${{ matrix.iris-source }}]"
 
     runs-on: ${{ matrix.os }}
 
@@ -123,14 +123,16 @@ jobs:
           env_name: ${{ env.ENV_NAME }}
           lock_file: ${{ env.LOCK_FILE }}
 
-      - name: "iris ${{ matrix.session }}"
+      - name: "iris-grib ${{ matrix.session }}"
         env:
           IRIS_SOURCE: ${{ matrix.iris-source }}
           PY_COLORS: 1
           PY_VER: ${{ matrix.python-version }}
         run: |
-          nox --session ${{ matrix.session }} -- --test-data-dir ${HOME}/iris-test-data/test_data
+          nox --session ${{ matrix.session }} -- ${{ matrix.coverage }} --test-data-dir ${HOME}/iris-test-data/test_data
 
-      - name: "Upload coverage report"
+      - name: "upload coverage report"
+        if: ${{ matrix.coverage }}
         uses: codecov/codecov-action@v4
-        if: ${{ matrix.coverage }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@
 | ⚙️ CI            | [![ci-manifest](https://github.com/SciTools/iris-grib/actions/workflows/ci-manifest.yml/badge.svg)](https://github.com/SciTools/iris-grib/actions/workflows/ci-manifest.yml) [![ci-tests](https://github.com/SciTools/iris-grib/actions/workflows/ci-tests.yml/badge.svg)](https://github.com/SciTools/iris-grib/actions/workflows/ci-tests.yml) [![pre-commit](https://results.pre-commit.ci/badge/github/SciTools/iris-grib/main.svg)](https://results.pre-commit.ci/latest/github/SciTools/iris-grib/main)                                                        |
 | 💬 Community     | [![GH Discussions](https://img.shields.io/badge/github-discussions%20%F0%9F%92%AC-yellow?logo=github&logoColor=lightgrey)](https://github.com/SciTools/iris-grib/discussions)                                                                                                                                                                                                                                                                                                                                                                                        |
 | 📖 Documentation | [![rtd](https://readthedocs.org/projects/iris-grib/badge/?version=latest)](https://iris-grib.readthedocs.io/en/latest/?badge=latest)                                                                                                                                                                                                                                                                                                                                                                                                                                 |
-| 📈 Health        | [![coveralls](https://coveralls.io/repos/github/SciTools/iris-grib/badge.svg?branch=main)](https://coveralls.io/github/SciTools/iris-grib?branch=main)                                                                                                                                                                                                                                                                                                                                                                                                               |
+| 📈 Health        | [![codecov](https://codecov.io/gh/SciTools/iris-grib/graph/badge.svg?token=5VtBaElXFW)](https://codecov.io/gh/SciTools/iris-grib)                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | ✨ Meta           | [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![NEP29](https://raster.shields.io/badge/follows-NEP29-orange.png)](https://numpy.org/neps/nep-0029-deprecation_policy.html) [![license - bds-3-clause](https://img.shields.io/github/license/SciTools/iris-grib)](https://github.com/SciTools/iris-grib/blob/main/LICENSE) [![conda platform](https://img.shields.io/conda/pn/conda-forge/iris-grib.svg)](https://anaconda.org/conda-forge/iris-grib) |
 | 📦 Package       | [![conda-forge](https://img.shields.io/conda/vn/conda-forge/iris-grib?color=orange&label=conda-forge&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/iris-grib) [![pypi](https://img.shields.io/pypi/v/iris-grib?color=orange&label=pypi&logo=python&logoColor=white)](https://pypi.org/project/iris-grib/) [![pypi - python version](https://img.shields.io/pypi/pyversions/iris-grib.svg?color=orange&logo=python&label=python&logoColor=white)](https://pypi.org/project/iris-grib/)                                                          |
 | 🧰 Repo          | [![commits-since](https://img.shields.io/github/commits-since/SciTools/iris-grib/latest.svg)](https://github.com/SciTools/iris-grib/commits/main) [![contributors](https://img.shields.io/github/contributors/SciTools/iris-grib)](https://github.com/SciTools/iris-grib/graphs/contributors) [![release](https://img.shields.io/github/v/release/scitools/iris-grib)](https://github.com/SciTools/iris-grib/releases)                                                                                                                                               |

diff --git a/noxfile.py b/noxfile.py
@@ -270,11 +270,15 @@ def tests(session: nox.sessions.Session, iris_source: str):
 
     session.run("python", "-m", "eccodes", "selfcheck")
 
-    session.run(
+    run_args = [
         "pytest",
         "--pyargs",
         "iris_grib",
-    )
+    ]
+
+    if "-c" in session.posargs or "--coverage" in session.posargs:
+        run_args.extend(["--cov=iris_grib", "--cov-report=xml"])
+    session.run(*run_args)
 
 
 @nox.session(python=PY_VER, venv_backend="conda")

diff --git a/pyproject.toml b/pyproject.toml
@@ -31,12 +31,13 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Atmospheric Science",
     "Topic :: Scientific/Engineering :: Visualization",
 ]
+description = "Functionality for converting between weather/climate datasets stored as GRIB files and SciTools-Iris Cubes"
 dynamic = [
     "dependencies",
+    "optional-dependencies",
     "readme",
     "version",
 ]
-description = "Functionality for converting between weather/climate datasets stored as GRIB files and SciTools-Iris Cubes"
 keywords = [
     "iris",
     "GRIB",
@@ -58,10 +59,12 @@ Issues = "https://github.com/SciTools/iris-grib/issues"
 license-files = ["LICENSE"]
 
 [tool.setuptools.dynamic]
-dependencies = {file = "requirements/core.txt"}
+dependencies = {file = "requirements/pypi-core.txt"}
 readme = {file = "README.md", content-type = "text/markdown"}
-optional-dependencies.all = {file = "requirements/all.txt"}
-optional-dependencies.test = {file = "requirements/test.txt"}
+
+[tool.setuptools.dynamic.optional-dependencies]
+dev = {file = "requirements/pypi-optional-dev.txt"}
+test = {file = "requirements/pypi-optional-test.txt"}
 
 [tool.setuptools.packages.find]
 include = ["iris_grib*"]

diff --git a/requirements/all.txt b/requirements/all.txt
diff --git a/requirements/core.txt b/requirements/core.txt
diff --git a/requirements/locks/py310-linux-64.lock b/requirements/locks/py310-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: bb88ce5d10a10e0a0df2ba8800b44ef1b44c069439153d3d6e424343ba556057
+# input_hash: 4c1c053d02dd4f1e5cf7ab187666840f573cfba8ed9387d768c66010531db165
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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@@ -76,15 +76,21 @@ https://conda.anaconda.org/conda-forge/linux-64/udunits2-2.2.28-h40f5838_3.conda
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-h8ee46fc_0.conda#077b6e8ad6a3ddb741fce2496dd01bec
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+https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.3.0-pyhd8ed1ab_0.conda#f42f433e48d6a715c0978b44a9219406
 https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda#5e4c0743c70186509d1412e03c2d8dfa
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+https://conda.anaconda.org/conda-forge/noarch/cachetools-5.3.3-pyhd8ed1ab_0.conda#cd4c26c702a9bcdc70ff05b609ddacbe
 https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
+https://conda.anaconda.org/conda-forge/noarch/cfgv-3.3.1-pyhd8ed1ab_0.tar.bz2#ebb5f5f7dc4f1a3780ef7ea7738db08c
+https://conda.anaconda.org/conda-forge/linux-64/chardet-5.2.0-py310hff52083_1.conda#a677136a83b823803d2f92045f885be2
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+https://conda.anaconda.org/conda-forge/linux-64/colorlog-6.8.2-py310hff52083_0.conda#db1be62a6a5d51f5a36fb99b2cc12972
 https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
+https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda#db16c66b759a64dc5183d69cc3745a52
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@@ -103,6 +109,7 @@ https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.5-py310h2372a71_0
 https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyh9f0ad1d_0.tar.bz2#2ba8498c1018c1e9c61eb99b973dfe19
 https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda#7f2e286780f072ed750df46dc2631138
 https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda#248f521b64ce055e7feae3105e7abeb8
+https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.2.1-pyhd8ed1ab_0.conda#d478a8a3044cdff1aa6e62f9269cefe0
 https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda#d3483c8fc2dc2cc3f5cf43e26d60cabf
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 https://conda.anaconda.org/conda-forge/noarch/pygments-2.17.2-pyhd8ed1ab_0.conda#140a7f159396547e9799aa98f9f0742e
@@ -116,6 +123,7 @@ https://conda.anaconda.org/conda-forge/noarch/setuptools-69.5.1-pyhd8ed1ab_0.con
 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
 https://conda.anaconda.org/conda-forge/noarch/snowballstemmer-2.2.0-pyhd8ed1ab_0.tar.bz2#4d22a9315e78c6827f806065957d566e
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0.conda#da1d979339e2714c30a8e806a33ec087
+https://conda.anaconda.org/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_0.tar.bz2#f832c45a477c78bebd107098db465095
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96
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 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.11.0-pyha770c72_0.conda#6ef2fc37559256cf682d8b3375e89b80
@@ -126,42 +134,53 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_10
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+https://conda.anaconda.org/conda-forge/linux-64/coverage-7.5.0-py310hc51659f_0.conda#3609fdb03842f67e2ec68a9c137221b8
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 https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.5-nompi_py310hba70d50_100.conda#e19392760c7e4da3b9cb0ee5bf61bc4b
+https://conda.anaconda.org/conda-forge/noarch/nox-2024.4.15-pyhff2d567_0.conda#600c0de12125f473d8099c0b3e6f88d4
+https://conda.anaconda.org/conda-forge/noarch/pre-commit-3.7.0-pyha770c72_0.conda#846ba0877cda9c4f11e13720cacd1968
 https://conda.anaconda.org/conda-forge/linux-64/cartopy-0.23.0-py310hcc13569_0.conda#89a13de526ea3008341e3a2aeab4da7e
 https://conda.anaconda.org/conda-forge/linux-64/python-eccodes-1.7.0-py310h1f7b6fc_1.conda#f020ac07b7df9c4b0bd0ece3055b5bd2
 https://conda.anaconda.org/conda-forge/noarch/iris-3.9.0-pyha770c72_0.conda#efaf150eb009f04efa58f1401c767192