Merge branch 'master' into am/classifier_labels

.github/release.yml

@@ -9,6 +9,9 @@ changelog:
     - title: New Features
       labels:
         - changelog-enhancement
+    - title: Bug Fixes
+      labels:
+        - bug
     - title: Other Changes
       labels:
         - "*"

.github/workflows/link_issue.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Verify Linked Issue
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.GITHUB_TOKEN}}
           script: |

.github/workflows/main.yml

@@ -28,8 +28,6 @@ jobs:
           # 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:

.github/workflows/publish.yml

@@ -95,6 +95,40 @@ jobs:
         '${{ github.ref_name }}' dist/**
         --repo '${{ github.repository }}'
 
+  build-for-prefix:
+    name: Build prefix package
+    needs:
+    - build
+    - install
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download the built dist
+        uses: actions/download-artifact@v4
+        with:
+          name: pip-dist
+          path: dist/
+      - name: Add tag to recipe
+        run: sed -i "s/TAG_VERSION/${{ github.ref_name }}/g" publish/recipes/release/ecoscope.yaml
+      - name: Add dist to recipe
+        run: sed -i "s/DIST_NAME/$(find ./dist/*.tar.gz  -printf "%f\n")/g" publish/recipes/release/ecoscope.yaml
+      - name: Log the generated recipe
+        run: cat publish/recipes/release/ecoscope.yaml
+      - name: Create channel
+        run: mkdir -p /tmp/ecoscope/release/artifacts
+      - name: Build prefix release
+        uses: prefix-dev/[email protected]
+        with:
+          recipe-path: publish/recipes/release/ecoscope.yaml
+          build-args: --output-dir /tmp/ecoscope/release/artifacts --channel https://prefix.dev/ecoscope-workflows --channel conda-forge
+      - run: |
+          for file in /tmp/ecoscope/release/artifacts/**/*.conda; do
+            rattler-build upload prefix -c ecoscope-workflows "$file"
+          done
+        env:
+          PREFIX_API_KEY: ${{ secrets.PREFIX_API_KEY }}
+
   publish-to-pypi:
     name: Publish to PyPI
     needs:

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].5' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /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].5' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].8' &> /dev/null"
    ]
   },
   {

ecoscope/base/base.py

@@ -412,6 +412,7 @@ def _create_trajsegments(gdf):
                 "heading": track_properties.heading,
                 "geometry": shapely.linestrings(coords),
                 "junk_status": gdf.junk_status,
+                "nsd": track_properties.nsd,
             },
             crs=4326,
             index=gdf.index,
@@ -625,6 +626,13 @@ def dist_meters(self):
                 _, _, distance = self.inverse_transformation
                 return distance
 
+            @property
+            def nsd(self):
+                start_point = df["geometry"].iloc[0]
+                geod = Geod(ellps="WGS84")
+                geod_displacement = [geod.inv(start_point.x, start_point.y, geo.x, geo.y)[2] for geo in df["_geometry"]]
+                return [(x**2) / (1000 * 2) for x in geod_displacement]
+
             @property
             def timespan_seconds(self):
                 return (df["_fixtime"] - df["fixtime"]).dt.total_seconds()

ecoscope/io/async_earthranger.py

@@ -6,6 +6,7 @@
 import ecoscope
 from ecoscope.io.utils import to_hex
 from ecoscope.io.earthranger_utils import clean_kwargs, to_gdf, clean_time_cols
+from erclient.client import ERClientException, ERClientNotFound
 
 try:
     from erclient.client import AsyncERClient
@@ -30,6 +31,28 @@ def __init__(self, sub_page_size=4000, tcp_limit=5, **kwargs):
         kwargs["client_id"] = kwargs.get("client_id", "das_web_client")
         super().__init__(**kwargs)
 
+    @classmethod
+    async def create(cls, **kwargs):
+        client = cls(**kwargs)
+
+        await client._init_client()
+        return client
+
+    async def _init_client(self):
+        if not self.auth:
+            try:
+                await self.login()
+            except ERClientNotFound:
+                raise ERClientNotFound("Failed login. Check Stack Trace for specific reason.")
+        else:
+            try:
+                await self.get_me()
+            except ERClientException:
+                raise ERClientException("Authorization token is invalid or expired.")
+
+    async def get_me(self):
+        return await self._get("user/me", params={})
+
     async def get_sources(
         self,
         manufacturer_id=None,

ecoscope/io/earthranger.py

@@ -34,22 +34,29 @@ def __init__(self, sub_page_size=4000, tcp_limit=5, **kwargs):
         self.tcp_limit = tcp_limit
         kwargs["client_id"] = kwargs.get("client_id", "das_web_client")
         super().__init__(**kwargs)
-        try:
-            self.login()
-        except ERClientNotFound:
-            raise ERClientNotFound("Failed login. Check Stack Trace for specific reason.")
+
+        if not self.auth:
+            try:
+                self.login()
+            except ERClientNotFound:
+                raise ERClientNotFound("Failed login. Check Stack Trace for specific reason.")
+        else:
+            try:
+                self.get_me()
+            except ERClientException:
+                raise ERClientException("Authorization token is invalid or expired.")
 
     def _token_request(self, payload):
         response = requests.post(self.token_url, data=payload)
         if response.ok:
-            self.auth = json.loads(response.text)
+            self.auth = response.json()
             expires_in = int(self.auth["expires_in"]) - 5 * 60
             self.auth_expires = pytz.utc.localize(datetime.datetime.utcnow()) + datetime.timedelta(seconds=expires_in)
             return True
 
         self.auth = None
         self.auth_expires = pytz.utc.localize(datetime.datetime.min)
-        raise ERClientNotFound(json.loads(response.text)["error_description"])
+        raise ERClientNotFound(response.json().get("error_description", "invalid token"))
 
     """
     GET Functions

ecoscope/mapping/map.py

@@ -493,7 +493,7 @@ def pil_layer(image, bounds, opacity=1):
         return layer
 
     @staticmethod
-    def get_named_tile_layer(layer: str) -> BitmapTileLayer:
+    def get_named_tile_layer(layer: str, opacity: float = 1) -> BitmapTileLayer:
         # From Leafmap
         # https://github.com/opengeos/leafmap/blob/master/leafmap/basemaps.py
         xyz_tiles = {
@@ -534,6 +534,7 @@ def get_named_tile_layer(layer: str) -> BitmapTileLayer:
             max_zoom=layer.get("max_zoom", None),
             min_zoom=layer.get("min_zoom", None),
             max_requests=layer.get("max_requests", None),
+            opacity=opacity,
         )
 
     def to_html(

publish/recipes/release/ecoscope.yaml

@@ -0,0 +1,73 @@
+context:
+  name: ecoscope
+  version: TAG_VERSION
+
+package:
+  name: ecoscope
+  version: ${{ version }}
+
+source:
+  path: ../../../dist/DIST_NAME
+
+build:
+  noarch: python
+  script: SETUPTOOLS_SCM_PRETEND_VERSION=${{ version }} pip install . -v
+  number: 5
+
+requirements:
+  host:
+    - python
+    - setuptools >=45
+    - setuptools-scm >=6.2
+    - pip
+  run:
+    - python
+    - backoff
+    - earthengine-api
+    - earthranger-client
+    - fiona <1.10.0
+    - geopandas <=0.14.2
+    - numpy <2  # added by me, but should be ensured by geopandas anyway
+    - pyproj
+    - rasterio
+    - tqdm
+    # ~ analysis ~
+    - astroplan
+    # - datashader  # (cisaacstern) per atmorling, not required for current workflows
+    - igraph
+    - mapclassify
+    # - matplotlib  # disabling in favor of matplotlib-base which is smaller
+    - matplotlib-base
+    - networkx
+    - numba
+    - scipy
+    - scikit-image
+    - scikit-learn
+    # ~ plotting ~
+    # - kaleido  # not available on conda and do we actually use this?
+    - plotly
+    # - scikit-learn  # duplicate with analysis
+    # ~ mapping ~
+    - lonboard==0.0.3
+    # - matplotlib  # duplicate with analysis
+    # - mapclassify  # duplicate with analysis
+
+tests:
+  - python:
+      imports:
+        - ecoscope
+        - ecoscope.analysis
+        - ecoscope.base
+        - ecoscope.io
+        - ecoscope.mapping
+        - ecoscope.plotting
+
+about:
+  summary: Standard Analytical Reporting Framework for Conservation
+  license: BSD-3-Clause
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - cisaacstern
+    - atmorling