Merge pull request #323 from tobac-project/RC_v1.5_hotfix

Merge `RC_v1.5_hotfix` into `main`
tobac-project · Sep 25, 2023 · 57385cd · 57385cd
2 parents d819159 + 513a074
commit 57385cd
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diff --git a/.github/workflows/check_notebooks.yml b/.github/workflows/check_notebooks.yml
@@ -12,13 +12,19 @@ jobs:
       - name: set up conda environment
         uses: conda-incubator/setup-miniconda@v2
         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: |
-          conda install -c conda-forge --yes ffmpeg gcc jupyter pytables
-          conda install -c conda-forge --yes --file example_requirements.txt
+          mamba install -c conda-forge --yes ffmpeg gcc jupyter pytables
+          mamba install -c conda-forge --yes --file example_requirements.txt
       - name: Install tobac
         run: |
           pip install .

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -3,5 +3,4 @@ formats: all
 python:
   version: 3
   install:
-    - requirements: doc/requirements.txt
-  system_packages: true
+    - requirements: doc/requirements.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,20 @@
 ### Tobac Changelog
 
+_**Version 1.5.1:**_
+
+**Bug fixes**
+
+- The `strict_thresholding` option in feature detection now works correctly for detecting minima, and produces the same results as without strict thresholding if the `n_min_threshold` is a scalar value [#316](https://github.com/tobac-project/tobac/pull/316)
+- utils.general.standardize_track_dataset was added back after being inadvertently removed in version 1.5.0 [#330](https://github.com/tobac-project/tobac/pull/330)
+- All Numba import errors are now caught with the exception of KeyboardInterrupts. [#335](https://github.com/tobac-project/tobac/pull/335)
+
+**Documentation**
+- Fix to readthedocs building after system packages no longer imported [#336](https://github.com/tobac-project/tobac/pull/336)
+
+**Repository Enhancements**
+- Fix to Jupyter Notebook CI that was timing out due to installing packages with `conda`, switched to `mamba` to resolve. [#340](https://github.com/tobac-project/tobac/pull/340)
+
+
 _**Version 1.5.0:**_
 
 **Enhancements for Users**

diff --git a/doc/feature_detection/notebooks/feature_detection_filtering.ipynb b/doc/feature_detection/notebooks/feature_detection_filtering.ipynb
@@ -26,10 +26,10 @@
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-     "iopub.status.idle": "2023-07-11T00:01:51.687071Z",
-     "shell.execute_reply": "2023-07-11T00:01:51.686080Z"
+     "iopub.execute_input": "2023-08-15T16:14:07.185005Z",
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+     "shell.execute_reply": "2023-08-15T16:14:13.773916Z"
     }
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    "outputs": [],
@@ -62,10 +62,10 @@
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-     "iopub.status.idle": "2023-07-11T00:01:51.919529Z",
-     "shell.execute_reply": "2023-07-11T00:01:51.918566Z"
+     "iopub.execute_input": "2023-08-15T16:14:13.779200Z",
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     }
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    "outputs": [
@@ -101,10 +101,10 @@
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-     "shell.execute_reply": "2023-07-11T00:01:52.323887Z"
+     "iopub.execute_input": "2023-08-15T16:14:14.072818Z",
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+     "shell.execute_reply": "2023-08-15T16:14:15.123554Z"
     }
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    "outputs": [],
@@ -135,10 +135,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:01:52.329156Z",
-     "iopub.status.busy": "2023-07-11T00:01:52.328875Z",
-     "iopub.status.idle": "2023-07-11T00:01:56.341645Z",
-     "shell.execute_reply": "2023-07-11T00:01:56.335837Z"
+     "iopub.execute_input": "2023-08-15T16:14:15.129205Z",
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+     "iopub.status.idle": "2023-08-15T16:14:16.832504Z",
+     "shell.execute_reply": "2023-08-15T16:14:16.828647Z"
     }
    },
    "outputs": [
@@ -196,10 +196,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:01:56.348391Z",
-     "iopub.status.busy": "2023-07-11T00:01:56.346681Z",
-     "iopub.status.idle": "2023-07-11T00:01:57.961544Z",
-     "shell.execute_reply": "2023-07-11T00:01:57.960460Z"
+     "iopub.execute_input": "2023-08-15T16:14:16.838887Z",
+     "iopub.status.busy": "2023-08-15T16:14:16.838617Z",
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+     "shell.execute_reply": "2023-08-15T16:14:18.821111Z"
     }
    },
    "outputs": [

diff --git a/doc/feature_detection/notebooks/multiple_thresholds_example.ipynb b/doc/feature_detection/notebooks/multiple_thresholds_example.ipynb
@@ -19,10 +19,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:02:04.454435Z",
-     "iopub.status.busy": "2023-07-11T00:02:04.453782Z",
-     "iopub.status.idle": "2023-07-11T00:02:09.305142Z",
-     "shell.execute_reply": "2023-07-11T00:02:09.303956Z"
+     "iopub.execute_input": "2023-08-15T16:14:27.894065Z",
+     "iopub.status.busy": "2023-08-15T16:14:27.893581Z",
+     "iopub.status.idle": "2023-08-15T16:14:38.976596Z",
+     "shell.execute_reply": "2023-08-15T16:14:38.975681Z"
     }
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    "outputs": [],
@@ -53,10 +53,10 @@
    "execution_count": 2,
    "metadata": {
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-     "iopub.execute_input": "2023-07-11T00:02:09.308788Z",
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-     "iopub.status.idle": "2023-07-11T00:02:09.531767Z",
-     "shell.execute_reply": "2023-07-11T00:02:09.531142Z"
+     "iopub.execute_input": "2023-08-15T16:14:38.981371Z",
+     "iopub.status.busy": "2023-08-15T16:14:38.980828Z",
+     "iopub.status.idle": "2023-08-15T16:14:39.374743Z",
+     "shell.execute_reply": "2023-08-15T16:14:39.373872Z"
     }
    },
    "outputs": [
@@ -101,10 +101,10 @@
    "execution_count": 3,
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     "execution": {
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-     "shell.execute_reply": "2023-07-11T00:02:10.040289Z"
+     "iopub.execute_input": "2023-08-15T16:14:39.462543Z",
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     }
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    "outputs": [],
@@ -132,10 +132,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:02:10.049518Z",
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     }
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    "outputs": [
@@ -175,10 +175,10 @@
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-     "iopub.execute_input": "2023-07-11T00:02:10.421989Z",
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-     "iopub.status.idle": "2023-07-11T00:02:10.742500Z",
-     "shell.execute_reply": "2023-07-11T00:02:10.741720Z"
+     "iopub.execute_input": "2023-08-15T16:14:41.615868Z",
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    "outputs": [
@@ -233,10 +233,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:02:10.745804Z",
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-     "shell.execute_reply": "2023-07-11T00:02:11.049631Z"
+     "iopub.execute_input": "2023-08-15T16:14:41.961925Z",
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     }
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    "outputs": [
@@ -277,10 +277,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:02:11.054792Z",
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-     "shell.execute_reply": "2023-07-11T00:02:11.463418Z"
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     }
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    "outputs": [
@@ -314,10 +314,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-07-11T00:02:11.466933Z",
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     }
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    "outputs": [

diff --git a/doc/feature_detection/notebooks/n_min_threshold_example.ipynb b/doc/feature_detection/notebooks/n_min_threshold_example.ipynb
@@ -19,10 +19,10 @@
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-     "shell.execute_reply": "2023-07-11T00:01:23.155547Z"
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    "outputs": [],
@@ -53,10 +53,10 @@
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+     "iopub.execute_input": "2023-08-15T16:13:40.674527Z",
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@@ -94,10 +94,10 @@
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@@ -132,10 +132,10 @@
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@@ -196,10 +196,10 @@
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@@ -254,10 +254,10 @@
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@@ -312,10 +312,10 @@
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@@ -379,10 +379,10 @@
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@@ -453,10 +453,10 @@
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@@ -501,10 +501,10 @@
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