Merge remote-tracking branch 'upstream/main' into v160_merge_main

tobac-project · Jan 6, 2025 · ad8d41a · ad8d41a
2 parents 5a9190e + be72676
commit ad8d41a
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diff --git a/.github/workflows/check_notebooks.yml b/.github/workflows/check_notebooks.yml
@@ -9,22 +9,13 @@ jobs:
     steps:
       - name: check out repository code
         uses: actions/checkout@v3
-      - name: set up conda environment
-        uses: conda-incubator/setup-miniconda@v2
+      - name: set up mamba environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-version: latest
-          miniforge-variant: mambaforge
-          channel-priority: strict
-          channels: conda-forge
-          show-channel-urls: true
-          use-only-tar-bz2: true
-          auto-update-conda: true
-          auto-activate-base: false
-          activate-environment: notebook-env
-      - name: Install tobac dependencies
-        run: |
-          mamba install -c conda-forge --yes ffmpeg gcc jupyter pytables
-          mamba install -c conda-forge --yes --file example_requirements.txt
+          environment-file: environment-examples.yml
+          generate-run-shell: true
+          cache-environment: true
+          cache-downloads: true
       - name: Install tobac
         run: |
           pip install .

diff --git a/.github/workflows/codecov-CI.yml b/.github/workflows/codecov-CI.yml
@@ -7,24 +7,20 @@ jobs:
     runs-on: ubuntu-latest
     env:
       OS: ubuntu-latest
-      PYTHON: "3.9"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       # Similar to MetPy install-conda action
       - name: Set up conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-version: latest
-          miniforge-variant: mambaforge
-          channel-priority: strict
-          channels: conda-forge
-          show-channel-urls: true
-          use-only-tar-bz2: true
+          environment-file: environment-ci.yml
+          generate-run-shell: true
+          cache-environment: true
+          cache-downloads: true
 
-      - name: Install dependencies and generate report
-        shell: bash -l {0}
+      - name: Generate report
+        shell: micromamba-shell {0}
         run:
-          mamba install --quiet --yes --file requirements.txt coverage pytest-cov &&
           python -m coverage run -m pytest --cov=./ --cov-report=xml
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v4

diff --git a/.github/workflows/matrix_ci.yml b/.github/workflows/matrix_ci.yml
@@ -35,7 +35,7 @@ jobs:
           cache-downloads: true
           channels: conda-forge
           channel-priority: strict
-          python-version: ${{ matrix.python-version }}
+          create-args: python=${{ matrix.python-version }}
 
       - name: Fetch all history for all tags and branches
         run: |

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
@@ -7,32 +7,27 @@ permissions:
   pull-requests: write
 
 jobs:
-  build:
+  lint-workflow:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - name: Check out Git repository
-        uses: actions/checkout@v3
-
-      - name: Set up conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/checkout@v4
+      - name: Set up mamba environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniforge-version: latest
-          miniforge-variant: mambaforge
-          channel-priority: strict
-          channels: conda-forge
-          show-channel-urls: true
-          use-only-tar-bz2: true
-
-      - name: Install tobac and pylint
-        run: |
-          mamba install --yes pylint
+          environment-file: environment-ci.yml
+          generate-run-shell: true
+          cache-environment: true
+          cache-downloads: true
+      - name: Install tobac
+        run:
           pip install .
 
       - name: Store the PR branch
-        run: |
+        run:
           echo "SHA=$(git rev-parse "$GITHUB_SHA")" >> $GITHUB_OUTPUT
         id: git
 
@@ -42,7 +37,7 @@ jobs:
           ref: ${{ github.base_ref }}
 
       - name: Get pylint score of RC branch
-        run: |
+        run:
           pylint tobac --disable=C --exit-zero
         id: main_score
 
@@ -52,7 +47,7 @@ jobs:
           ref: "${{ steps.git.outputs.SHA }}"  
 
       - name: Get pylint score of PR branch
-        run: |
+        run:
           # use shell script to save only tail of output  
           OUTPUT_PART=$(pylint tobac --disable=C --exit-zero | tail -n 2)
           # but post entire output in the action details 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,29 +1,38 @@
 ### Tobac Changelog
 
+_**Version 1.5.5:**_
+
+**Bug fixes**
+
+- Including of annotations import for python versions before 3.10 [#468](https://github.com/tobac-project/tobac/pull/468)
+- Fix bulk statistics calculation when provided a dask array [#474](https://github.com/tobac-project/tobac/pull/474)
+
+**Internal Enhancements**
+
+- Fix matrix testing to use the specified python versions [#468](https://github.com/tobac-project/tobac/pull/468)
+
+
 _**Version 1.5.4:**_
 
 **Enhancements for Users**
 
 - Added the ability to use the Minimum Euclidean Spanning Tree merge/split method on data with periodic boundaries [#372](https://github.com/tobac-project/tobac/pull/372)
 - Added the ability to calculate online bulk statistics during feature detection on the raw (i.e., unsmoothed) data [#449](https://github.com/tobac-project/tobac/pull/449)
 
-
 **Bug fixes**
 
 - Fixes to calculations of bulk statistics [#437](https://github.com/tobac-project/tobac/pull/437)
 - Fixes to handling of PBC feature points on the PBC wraparound border [#434](https://github.com/tobac-project/tobac/pull/434)
 - Fixed an error that allows non-matching features to be used in the offline bulk statistics calculation [#448](https://github.com/tobac-project/tobac/pull/448)
 - Fixed a bug that prevented using minimum distance filtering with varying vertical coordinates [#452](https://github.com/tobac-project/tobac/pull/452)
 
-
 **Documentation**
 
 - Add thumbnails to the new example gallery [#428](https://github.com/tobac-project/tobac/pull/428)
 - Added documentation for developers [#281](https://github.com/tobac-project/tobac/pull/281)
 - Updated documentation for the `n_min_threshold` function in feature detection [#432](https://github.com/tobac-project/tobac/pull/432)
 - Added documentation for dealing with big datasets [#408](https://github.com/tobac-project/tobac/pull/408)
-- Updated documentation to note that the *tobac* v1.5.0 paper in GMD is in its final form [#450](https://github.com/tobac-project/tobac/pull/450)
-- 
+- Updated documentation to note that the *tobac* v1.5.0 paper in GMD is in its final form [#450](https://github.com/tobac-project/tobac/pull/450) 
 
 **Internal Enhancements**
 
@@ -33,8 +42,6 @@ _**Version 1.5.4:**_
 - Resolved issues around updating dependencies in `black` formatting checks and Zenodo JSON checks [#457](https://github.com/tobac-project/tobac/pull/457)
 
 
-
-
 _**Version 1.5.3:**_
 
 **Enhancements for Users**

diff --git a/dev_requirements.txt b/dev_requirements.txt
@@ -13,3 +13,4 @@ pre-commit
 black
 pytest
 typing_extensions
+nbconvert
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,3 +13,4 @@ pre-commit @@
     black
     pytest
     typing_extensions
+    nbconvert