Merge pull request #144 from tobac-project/dev

Merge `dev` into `main` for 1.3.1 release
tobac-project · Jun 27, 2022 · e6e8fc3 · e6e8fc3
2 parents 0d098ac + fee0208
commit e6e8fc3
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,12 @@
+* [ ] Have you followed our guidelines in CONTRIBUTING.md? 
+* [ ] Have you self-reviewed your code and corrected any misspellings? 
+* [ ] Have you written documentation that is easy to understand?
+* [ ] Have you written descriptive commit messages? 
+* [ ] Have you added NumPy docstrings for newly added functions? 
+* [ ] Have you formatted your code using black? 
+* [ ] If you have introduced a new functionality, have you added adequate unit tests?
+* [ ] Have all tests passed in your local clone? 
+* [ ] If you have introduced a new functionality, have you added an example notebook?
+* [ ] Have you kept your pull request small and limited so that it is easy to review? 
+* [ ] Have the newest changes from this branch been merged? 
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,19 @@
 ### Tobac Changelog
 
+_**Version 1.3.1:**_
+
+**Enhancements**
+
+- Added auto-downloading of files in the example notebooks if data isn't already present [#113](https://github.com/tobac-project/tobac/pull/113)
+
+**Bug fixes**
+
+- Fixed a bug with `map_tracks` that had it plot untracked cells caused by the switch to `-1` for untracked cells [#130](https://github.com/tobac-project/tobac/pull/130)
+
+**Repository enhancements**
+
+- New pull request template for the repository, including a checklist to be completed for each pull request [#120](https://github.com/tobac-project/tobac/pull/120)
+
 _**Version 1.3:**_
 
 **Enhancements**

diff --git a/examples/Example_OLR_Tracking_model/Example_OLR_Tracking_model.ipynb b/examples/Example_OLR_Tracking_model/Example_OLR_Tracking_model.ipynb
@@ -30,14 +30,13 @@
     "import iris\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import os,sys\n",
     "import matplotlib.pyplot as plt\n",
     "import iris.plot as iplt\n",
     "import iris.quickplot as qplt\n",
-    "import zipfile, shutil\n",
+    "import shutil\n",
     "import datetime\n",
     "from six.moves import urllib\n",
-    "from glob import glob\n",
+    "from pathlib import Path\n",
     "%matplotlib inline"
    ]
   },
@@ -62,7 +61,7 @@
     "warnings.filterwarnings('ignore', category=UserWarning, append=True)\n",
     "warnings.filterwarnings('ignore', category=RuntimeWarning, append=True)\n",
     "warnings.filterwarnings('ignore', category=FutureWarning, append=True)\n",
-    "warnings.filterwarnings('ignore',category=pd.io.pytables.PerformanceWarning)\n"
+    "warnings.filterwarnings('ignore',category=pd.io.pytables.PerformanceWarning)"
    ]
   },
   {
@@ -79,62 +78,63 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_out='../'"
+    "data_out=Path('../')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "start downloading data\n",
+      "start extracting data\n",
+      "data extracted\n"
+     ]
+    }
+   ],
    "source": [
-    "# # Download the data: This only has to be done once for all tobac examples and can take a while\n",
-    "# file_path='https://zenodo.org/record/3195910/files/climate-processes/tobac_example_data-v1.0.1.zip'\n",
-    "# #file_path='http://zenodo..'\n",
-    "# tempfile='temp.zip'\n",
-    "# print('start downloading data')\n",
-    "# request=urllib.request.urlretrieve(file_path,tempfile)\n",
-    "# print('start extracting data')\n",
-    "# shutil.unpack_archive(tempfile,data_out)\n",
-    "# #zf = zipfile.ZipFile(tempfile)\n",
-    "# #zf.extractall(data_out)\n",
-    "# os.remove(tempfile)\n",
-    "# print('data extracted')\n"
+    "# Download the data: This only has to be done once for all tobac examples and can take a while\n",
+    "data_file = list(data_out.rglob('data/Example_input_OLR_model.nc'))\n",
+    "if len(data_file) == 0:\n",
+    "    file_path='https://zenodo.org/record/3195910/files/climate-processes/tobac_example_data-v1.0.1.zip'\n",
+    "    #file_path='http://zenodo..'\n",
+    "    tempfile=Path('temp.zip')\n",
+    "    print('start downloading data')\n",
+    "    request=urllib.request.urlretrieve(file_path, tempfile)\n",
+    "    print('start extracting data')\n",
+    "    shutil.unpack_archive(tempfile, data_out)\n",
+    "    tempfile.unlink()\n",
+    "    print('data extracted')\n",
+    "    data_file = list(data_out.rglob('data/Example_input_OLR_model.nc'))"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 6,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "data_file=os.path.join(data_out,'*','data','Example_input_OLR_model.nc')\n",
-    "data_file = glob(data_file)[0]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [],
    "source": [
     "#Load Data from downloaded file:\n",
-    "OLR=iris.load_cube(data_file,'OLR')"
+    "OLR=iris.load_cube(data_file[0],'OLR')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
     "#Set up directory to save output and plots:\n",
-    "savedir='Save'\n",
-    "if not os.path.exists(savedir):\n",
-    "    os.makedirs(savedir)\n",
-    "plot_dir=\"Plot\"\n",
-    "if not os.path.exists(plot_dir):\n",
-    "    os.makedirs(plot_dir)"
+    "savedir=Path(\"Save\")\n",
+    "if not savedir.is_dir():\n",
+    "    savedir.mkdir()\n",
+    "plot_dir=Path(\"Plot\")\n",
+    "if not plot_dir.is_dir():\n",
+    "    plot_dir.mkdir()"
    ]
   },
   {
@@ -147,7 +147,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -157,7 +157,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -187,9 +187,9 @@
    "source": [
     "# Perform feature detection:\n",
     "print('starting feature detection')\n",
-    "Features=tobac.feature_detection_multithreshold(OLR,dxy,**parameters_features)\n",
-    "Features.to_hdf(os.path.join(savedir,'Features.h5'),'table')\n",
-    "print('feature detection performed and saved')\n"
+    "Features=tobac.feature_detection_multithreshold(OLR,dxy, **parameters_features)\n",
+    "Features.to_hdf(savedir / 'Features.h5', 'table')\n",
+    "print('feature detection performed and saved')"
    ]
   },
   {
@@ -202,7 +202,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -233,8 +233,8 @@
     "print('Starting segmentation based on OLR.')\n",
     "Mask_OLR,Features_OLR=tobac.segmentation_2D(Features,OLR,dxy,**parameters_segmentation)\n",
     "print('segmentation OLR performed, start saving results to files')\n",
-    "iris.save([Mask_OLR],os.path.join(savedir,'Mask_Segmentation_OLR.nc'),zlib=True,complevel=4)                \n",
-    "Features_OLR.to_hdf(os.path.join(savedir,'Features_OLR.h5'),'table')\n",
+    "iris.save([Mask_OLR], savedir / 'Mask_Segmentation_OLR.nc', zlib=True, complevel=4)                \n",
+    "Features_OLR.to_hdf(savedir / 'Features_OLR.h5', 'table')\n",
     "print('segmentation OLR performed and saved')"
    ]
   },
@@ -248,7 +248,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -267,21 +267,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Frame 95: 18 trajectories present.\n"
+      "Frame 95: 12 trajectories present.\n"
      ]
     }
    ],
    "source": [
     "# Perform linking and save results to file:\n",
-    "Track=tobac.linking_trackpy(Features,OLR,dt=dt,dxy=dxy,**parameters_linking)\n",
-    "Track.to_hdf(os.path.join(savedir,'Track.h5'),'table')"
+    "Track=tobac.linking_trackpy(Features, OLR, dt=dt, dxy=dxy, **parameters_linking)\n",
+    "Track.to_hdf(savedir / 'Track.h5', 'table')"
    ]
   },
   {
@@ -298,7 +298,7 @@
    "outputs": [],
    "source": [
     "# Set extent of maps created in the following cells:\n",
-    "axis_extent=[-95,-89,28,32]        "
+    "axis_extent = [-95, -89, 28, 32]        "
    ]
   },
   {
@@ -322,8 +322,8 @@
    "source": [
     "# Plot map with all individual tracks:\n",
     "import cartopy.crs as ccrs\n",
-    "fig_map,ax_map=plt.subplots(figsize=(10,10),subplot_kw={'projection': ccrs.PlateCarree()})\n",
-    "ax_map=tobac.map_tracks(Track,axis_extent=axis_extent,axes=ax_map)"
+    "fig_map, ax_map = plt.subplots(figsize=(10,10), subplot_kw={'projection': ccrs.PlateCarree()})\n",
+    "ax_map = tobac.map_tracks(Track, axis_extent=axis_extent,  axes=ax_map)"
    ]
   },
   {
@@ -357,7 +357,7 @@
    "outputs": [],
    "source": [
     "# # Save animation to file:\n",
-    "# savefile_animation=os.path.join(plot_dir,'Animation.mp4')\n",
+    "# savefile_animation = plot_dir /'Animation.mp4'\n",
     "# animation_test_tobac.save(savefile_animation,dpi=200)\n",
     "# print(f'animation saved to {savefile_animation}')"
    ]