Merge branch 'master' into mobt802_lightning_cell_method_consistency …

…to resolve Github action failures folowing known bug fix
metoppv · Dec 17, 2024 · 41b7f5c · 41b7f5c
2 parents 94c632f + 9b2db98
commit 41b7f5c
Show file tree

Hide file tree

Showing 13 changed files with 450 additions and 160 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,6 +3,8 @@ name: CI Tests
 on:
   pull_request:
   push:
+    branches:
+      - master  # Run tests only when changes are pushed to 'default'
   workflow_dispatch:
 jobs:
   Sphinx-Pytest-Coverage:
@@ -14,56 +16,44 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/cache@v4
-      id: cache
-      with:
-        path: /usr/share/miniconda/envs/im${{ matrix.env }}
-        key: ${{ format('{0}-conda-improver-{1}-{2}', runner.os, matrix.env, hashFiles(format('envs/{0}.yml', matrix.env))) }}
 
-    - name: conda env update
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda update -q -n base -c defaults conda
-        conda install -q -n base -c conda-forge -c nodefaults mamba
-        rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround for mamba-org/mamba#488
-        mamba env create -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }}
+    - name: Environment creation
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: envs/${{ matrix.env }}.yml
+        init-shell: bash
+        cache-environment: true
 
-    - name: conda info
+    - name: Environment info
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+      shell: bash -el {0}
 
     - name: sphinx documentation
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         make -C doc html SPHINXOPTS="-W --keep-going"
+      shell: micromamba-shell {0}
 
     - name: pytest without coverage
       if: matrix.env == 'conda-forge'
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         pytest
+      shell: micromamba-shell {0}
 
     - name: pytest with coverage
       if: matrix.env != 'conda-forge'
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         pytest --cov=improver --cov-report xml:coverage.xml
+      shell: micromamba-shell {0}
 
     - name: codacy upload
       if: env.CODACY_PROJECT_TOKEN && matrix.env == 'environment_a'
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         python-codacy-coverage -v -r coverage.xml
       env:
         CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+      shell: micromamba-shell {0}
 
     - name: codecov upload
       uses: codecov/codecov-action@v5
@@ -133,36 +123,25 @@ jobs:
 
     - uses: actions/checkout@v4
 
-    - uses: actions/cache@v4
-      id: cache
+    - name: Environment creation
+      uses: mamba-org/setup-micromamba@v2
       with:
-        path: /usr/share/miniconda/envs/im${{ matrix.env }}
-        key: ${{ format('{0}-conda-improver-{1}-{2}', runner.os, matrix.env, hashFiles(format('envs/{0}.yml', matrix.env))) }}
-
-    - name: conda env update
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda update -q -n base -c defaults conda
-        conda install -q -n base -c conda-forge mamba
-        rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround for mamba-org/mamba#488
-        mamba env create -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }}
+        environment-file: envs/${{ matrix.env }}.yml
+        init-shell: bash
+        cache-environment: true
 
-    - name: conda info
+    - name: Environment info
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+      shell: bash -el {0}
 
     - name: safety
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         safety check || true
+      shell: micromamba-shell {0}
 
     - name: bandit
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         bandit -r improver
+      shell: micromamba-shell {0}
diff --git a/.github/workflows/scheduled.yml b/.github/workflows/scheduled.yml
@@ -6,113 +6,104 @@ on:
   schedule:
     - cron: '7 4 * * *'
   workflow_dispatch:
+
 jobs:
   Sphinx-Pytest-Coverage:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         env: [latest]
+
     if: github.repository_owner == 'metoppv'
     steps:
+
     - uses: actions/checkout@v4
-    - name: conda env update
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda update -q -n base -c defaults conda
-        conda install -q -n base -c conda-forge -c nodefaults mamba
-        rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround for mamba-org/mamba#488
-        mamba env create -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }}
-    - name: conda info
+
+    - name: Environment creation
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: envs/${{ matrix.env }}.yml
+        init-shell: bash
+        cache-environment: true
+
+    - name: Environment info
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+      shell: bash -el {0}
+
     - name: sphinx documentation
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         make -C doc html SPHINXOPTS="-W --keep-going"
+      shell: micromamba-shell {0}
+
     - name: pytest without coverage
-      if: matrix.env != 'environment_a'
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         pytest
-    - name: pytest with coverage
-      if: matrix.env == 'environment_a'
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        pytest --cov=improver --cov-report xml:coverage.xml
-    - name: codacy upload
-      if: env.CODACY_PROJECT_TOKEN && matrix.env == 'environment_a'
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        python-codacy-coverage -v -r coverage.xml
-      env:
-        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-    - name: codecov upload
-      uses: codecov/codecov-action@v5
-      if: matrix.env == 'environment_a'
+      shell: micromamba-shell {0}
+
   Safety-Bandit:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         env: [latest]
+
     if: github.repository_owner == 'metoppv'
     steps:
+
     - uses: actions/checkout@v4
-    - name: conda env update
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda update -q -n base -c defaults conda
-        conda install -q -n base -c conda-forge -c nodefaults mamba
-        rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround for mamba-org/mamba#488
-        mamba env create -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }}
-    - name: conda info
+
+    - name: Environment creation
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: envs/${{ matrix.env }}.yml
+        init-shell: bash
+        cache-environment: true
+
+    - name: Environment info
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+      shell: bash -el {0}
+
     - name: safety
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         safety check || true
+      shell: micromamba-shell {0}
+
     - name: bandit
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         bandit -r improver
+      shell: micromamba-shell {0}
+
   Type-checking:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         env: [latest]
+
     if: github.repository_owner == 'metoppv'
     steps:
+
     - uses: actions/checkout@v4
-    - name: conda env update
-      run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda update -q -n base -c defaults conda
-        conda install -q -n base -c conda-forge -c nodefaults mamba
-        rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround for mamba-org/mamba#488
-        mamba env create -q --file envs/${{ matrix.env }}.yml --name im${{ matrix.env }}
-    - name: conda info
+
+    - name: Environment creation
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: envs/${{ matrix.env }}.yml
+        init-shell: bash
+        cache-environment: true
+
+    - name: Environment info
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+      shell: bash -el {0}
+
     - name: mypy
       run: |
-        source '/usr/share/miniconda/etc/profile.d/conda.sh'
-        conda activate im${{ matrix.env }}
         mypy improver || true
+      shell: micromamba-shell {0}
diff --git a/.mailmap b/.mailmap
@@ -30,6 +30,8 @@ Meabh NicGuidhir <[email protected]> <meabh.nicguidhir@metoffice
 Neil Crosswaite <[email protected]> <[email protected]>
 Paul Abernethy <[email protected]> <[email protected]>
 Peter Jordan <[email protected]> <[email protected]>
+Phil Relton <[email protected]> <[email protected]>
+Phoebe Lambert <[email protected]> <[email protected]>
 Sam Griffiths <[email protected]> <[email protected]>
 Shafiat Dewan <[email protected]> <[email protected]>
 Shubhendra Singh Chauhan <[email protected]> <[email protected]>

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -59,13 +59,15 @@ below:
  - Caroline Jones (Met Office, UK)
  - Peter Jordan (Met Office, UK)
  - Bruno P. Kinoshita (NIWA, NZ)
+ - Phoebe Lambert (Met Office, UK)
  - Lucy Liu (Bureau of Meteorology, Australia)
  - Daniel Mentiplay (Bureau of Meteorology, Australia)
  - Stephen Moseley (Met Office, UK)
  - Meabh NicGuidhir (Met Office, UK)
  - Benjamin Owen (Bureau of Meteorology, Australia)
  - Carwyn Pelley (Met Office, UK)
  - Tim Pillinger (Met Office, UK)
+ - Phil Relton (Met Office, UK)
  - Fiona Rust (Met Office, UK)
  - Chris Sampson (Met Office, UK)
  - Caroline Sandford (Met Office, UK)

diff --git a/envs/conda-forge.yml b/envs/conda-forge.yml
@@ -25,6 +25,7 @@ dependencies:
   - bandit
   - filelock
   - pytest
+  - setuptools
   - sphinx-autodoc-typehints
   - sphinx_rtd_theme
   - threadpoolctl

diff --git a/envs/environment_a.yml b/envs/environment_a.yml
@@ -2,6 +2,7 @@
 name: improver_a
 channels:
   - conda-forge
+  - main
 dependencies:
   - python=3.7
   # Required
@@ -37,4 +38,4 @@ dependencies:
   - safety
   - sphinx-autodoc-typehints
   - sphinx_rtd_theme
-  - threadpoolctl
+  - threadpoolctl
diff --git a/improver/standardise.py b/improver/standardise.py
@@ -236,6 +236,15 @@ def _discard_redundant_cell_methods(cube: Cube) -> None:
 
         cube.cell_methods = updated_cms
 
+    @staticmethod
+    def _remove_long_name_if_standard_name(cube: Cube) -> None:
+        """
+        Remove the long_name attribute from cubes if the cube also has a standard_name defined
+        """
+
+        if cube.standard_name and cube.long_name:
+            cube.long_name = None
+
     def process(self, cube: Cube) -> Cube:
         """
         Perform compulsory and user-configurable metadata adjustments.  The
@@ -269,6 +278,7 @@ def process(self, cube: Cube) -> Cube:
         if self._attributes_dict:
             amend_attributes(cube, self._attributes_dict)
         self._discard_redundant_cell_methods(cube)
+        self._remove_long_name_if_standard_name(cube)
 
         # this must be done after unit conversion as if the input is an integer
         # field, unit conversion outputs the new data as float64