Merge branch 'master' into am/classifier_labels

.github/workflows/main.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
     strategy:
       fail-fast: false
       matrix:
@@ -23,9 +23,13 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
+          # https://github.com/mamba-org/setup-micromamba/issues/227
+          micromamba-version: 1.5.10-0
           environment-file: ${{ matrix.env }}
+          cache-environment: true
+          cache-downloads: true
 
       - name: Test
         env:

doc/source/conf.py

@@ -106,7 +106,7 @@
 commit_id = subprocess.check_output(["git", "rev-parse", "--short", "HEAD"]).strip().decode("ascii")
 nbsphinx_prolog = f"""
 .. image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: {{{{ "https://githubtocolab.com/wildlife-dynamics/ecoscope/blob/{commit_id}/doc/source/" + env.docname|urlencode + ".ipynb" }}}}
+  :target: {{{{ "https://colab.research.google.com/github/wildlife-dynamics/ecoscope/blob/{commit_id}/doc/source/" + env.docname|urlencode + ".ipynb" }}}}
 
 ----
 """  # noqa

doc/source/notebooks/01. IO/EarthRanger_IO.ipynb

@@ -29,7 +29,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -614,7 +614,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "patrol_df = er_io.get_patrols()\n",
+    "patrol_df = er_io.get_patrols(\n",
+    "    since=pd.Timestamp(\"2017-01-01\").isoformat(),\n",
+    "    until=pd.Timestamp(\"2017-04-01\").isoformat(),\n",
+    ")\n",
+    "\n",
     "\n",
     "relocs = er_io.get_patrol_observations(\n",
     "    patrol_df,\n",
@@ -709,8 +713,8 @@
     ")\n",
     "\n",
     "if not elephants.empty:\n",
-    "    for i, value in elephants.iterrows():\n",
-    "        er_io.delete_observation(observation_id=elephants.loc[i, \"extra__id\"])"
+    "    for observation_id in elephants[\"extra__id\"].unique():\n",
+    "        er_io.delete_observation(observation_id)"
    ]
   },
   {
@@ -863,11 +867,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "relocs.drop(\n",
-    "    columns=relocs.columns[relocs.applymap(lambda x: isinstance(x, list)).any()],\n",
-    "    errors=\"ignore\",\n",
-    "    inplace=True,\n",
-    ")\n",
+    "relocs = relocs.select_dtypes(exclude=[list])\n",
     "\n",
     "relocs.to_file(os.path.join(output_dir, \"observations.gpkg\"), layer=\"observations\")"
    ]

doc/source/notebooks/01. IO/GEE_IO.ipynb

@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -38,7 +38,6 @@
    "source": [
     "import os\n",
     "import sys\n",
-    "import zipfile\n",
     "\n",
     "import shapely\n",
     "\n",
@@ -208,26 +207,9 @@
     "ecoscope.io.utils.download_file(\n",
     "    url=img.getDownloadUrl(download_config),\n",
     "    path=img_zip_file,\n",
+    "    unzip=True,\n",
     ")"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Unzip"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with zipfile.ZipFile(img_zip_file) as z:\n",
-    "    for name in z.namelist():\n",
-    "        z.extract(name, output_dir)"
-   ]
   }
  ],
  "metadata": {

doc/source/notebooks/01. IO/Landscape Dynamics Data.ipynb

@@ -29,7 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -40,7 +40,6 @@
    "source": [
     "import os\n",
     "import sys\n",
-    "import zipfile\n",
     "\n",
     "import geopandas as gpd\n",
     "\n",
@@ -90,25 +89,10 @@
     "    url=\"https://maraelephant.maps.arcgis.com/sharing/rest/content/items/162e299f0c7d472b8e36211e946bb273/data\",\n",
     "    path=output_dir,\n",
     "    overwrite_existing=False,\n",
+    "    unzip=True,\n",
     ")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Extract ZIP"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "zipfile.ZipFile(os.path.join(output_dir, \"active_public_uncategorized_shpfiles.zip\")).extractall(path=output_dir)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

doc/source/notebooks/02. Relocations & Trajectories/Relocations_and_Trajectories.ipynb

@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -252,7 +252,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "relocs[[\"groupby_col\", \"fixtime\", \"geometry\"]].explore()"
+    "relocs[[\"groupby_col\", \"geometry\"]].explore()"
    ]
   },
   {

doc/source/notebooks/03. Home Range & Movescape/EcoGraph.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -152,7 +152,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "traj.explore()"
+    "traj[\"geometry\"].explore()"
    ]
   },
   {
@@ -546,7 +546,7 @@
     "        individual=\"1d22ff96-44d4-45c4-adc3-db1513acbe7d\",\n",
     "        interpolation=\"dofjojfs\",\n",
     "    )\n",
-    "except NotImplemented as e:\n",
+    "except NotImplementedError as e:\n",
     "    print(e)"
    ]
   },

doc/source/notebooks/03. Home Range & Movescape/Elliptical Time Density (ETD).ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/03. Home Range & Movescape/Reduce Regions.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/04. EcoMap & EcoPlot/EcoMap.ipynb

@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/04. EcoMap & EcoPlot/EcoPlot.ipynb

@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {
@@ -98,7 +98,6 @@
     "ecoscope.io.download_file(\n",
     "    f\"{ECOSCOPE_RAW}/tests/sample_data/vector/er_relocs.csv.zip\",\n",
     "    os.path.join(output_dir, \"er_relocs.csv.zip\"),\n",
-    "    unzip=False,\n",
     ")\n",
     "\n",
     "data = pd.read_csv(os.path.join(output_dir, \"er_relocs.csv.zip\"), header=0, index_col=0)\n",

doc/source/notebooks/05. Environmental Analyses/Landscape Grid.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/05. Environmental Analyses/Remote Sensing Time Series Anomaly.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/05. Environmental Analyses/Seasonal Calculation.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/06. Data Management/Tracking Data Gantt Chart.ipynb

@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].3' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].5' &> /dev/null"
    ]
   },
   {

ecoscope/analysis/astronomy.py

@@ -1,7 +1,8 @@
 import warnings
+
 import numpy as np
-import pyproj
 import pandas as pd
+import pyproj
 
 try:
     import astroplan
@@ -109,4 +110,4 @@ def get_daynight_ratio(traj, n_grid_points=150) -> pd.Series:
     day_distance += (day_night_df.dist_meters * i).sum()
     night_distance += ((1 - i) * day_night_df.dist_meters).sum()
 
-    return day_distance / night_distance
+    return night_distance / day_distance

ecoscope/analysis/classifier.py

@@ -135,11 +135,22 @@ def apply_color_map(dataframe, input_column_name, cmap, output_column_name=None)
         cmap = mpl.colormaps[cmap]
         cmap = cmap.resampled(dataframe[input_column_name].nunique())
 
-        cmap_colors = cmap(range(dataframe[input_column_name].nunique()))
+        if pd.api.types.is_numeric_dtype(dataframe[input_column_name].dtype):
+            cmap_colors = []
+            val_min = dataframe[input_column_name].min()
+            val_max = dataframe[input_column_name].max()
+            for val in dataframe[input_column_name].unique():
+                cmap_colors.append(cmap((val - val_min) / (val_max - val_min)))
+        else:
+            cmap_colors = cmap(range(len(dataframe[input_column_name].unique())))
+
+        color_list = []
+        for color in cmap_colors:
+            color_list.append(tuple([round(val * 255) for val in color]))
 
         # convert to hex first to put values in range(0,255), then to an RGBA tuple
         cmap = pd.Series(
-            [hex_to_rgba(mpl.colors.to_hex(color)) for color in cmap_colors],
+            color_list,
             index=dataframe[input_column_name].unique(),
         )
 

ecoscope/analysis/ecograph.py

@@ -85,7 +85,7 @@ def compute(df):
             G = self._get_ecograph(df, subject_name, radius, cutoff, tortuosity_length)
             self.graphs[subject_name] = G
 
-        self.trajectory.groupby("groupby_col")[self.trajectory.columns].progress_apply(compute)
+        self.trajectory.groupby("groupby_col")[self.trajectory.columns].apply(compute)
 
     def to_csv(self, output_path):
         """

ecoscope/analysis/feature_density.py

@@ -1,3 +1,6 @@
+import numpy as np
+
+
 def calculate_feature_density(selection, grid, geometry_type="point"):
     def clip_density(cell):
         if geometry_type == "point":
@@ -12,5 +15,5 @@ def clip_density(cell):
             raise ValueError("Unsupported geometry type")
 
     grid["density"] = grid.geometry.apply(clip_density)
-    # grid["density"] = grid["density"].replace(0, np.nan)  # Set 0's to nan so they don't draw on map
+    grid["density"] = grid["density"].replace(0, np.nan)  # Set 0's to nan so they don't draw on map
     return grid