update Dockerfile and example configs

.gitignore

@@ -99,3 +99,4 @@ models/*
 test-obs*
 lib/vision_cache/*
 config.yml
+env.list

Dockerfile

@@ -1,4 +1,6 @@
-FROM python:3.10.5
+FROM python:3.11.6
+
+RUN apt-get update && apt-get install -y libgdal-dev
 
 RUN useradd -ms /bin/bash inaturalist
 USER inaturalist

app.py

@@ -8,9 +8,13 @@
     CONFIG = {
         "app_secret": os.environ["APP_SECRET"],
         "models": [{
+            "name": os.environ["MODEL_NAME"],
             "vision_model_path": os.environ["VISION_MODEL_PATH"],
             "taxonomy_path": os.environ["TAXONOMY_PATH"],
-            "tf_geo_model_path": os.environ["TF_GEO_MODEL_PATH"]
+            "tf_geo_elevation_model_path": os.environ["TF_GEO_MODEL_PATH"],
+            "elevation_h3_r4": os.environ["ELEVATION_H3_R4_PATH"],
+            "tf_elev_thresholds": os.environ["GEO_THRESHOLDS_PATH"],
+            "taxon_ranges_path": os.environ["TAXON_RANGES_PATH"]
         }]
     }
     if "GEO_MIN" in os.environ:

config.yml.example

@@ -1,6 +1,10 @@
 app_secret: "somesecret"
-vision_model_path: "models/.../model.h5"
-taxonomy_path: "models/.../taxonomy.csv"
-tf_geo_model_path: "models/.../tf_gpmodel.h5"
-pt_geo_model_path: "models/.../model.pth.tar"
-use_pt_gp_model: False
+models:
+  - name: "ModelGenerationName"
+    vision_model_path: "models/.../vision_model.h5"
+    taxonomy_path: "models/.../taxonomy.csv"
+    tf_geo_elevation_model_path: "models/.../tf_gpmodel.h5"
+    elevation_h3_r4: "models/.../elevation_r4_5m.csv"
+    tf_elev_thresholds: "models/.../thresholds.csv"
+    taxon_ranges_path: "models/.../taxon_ranges"
+    geo_min: 0.005

env.list.example

@@ -1,4 +1,9 @@
 APP_SECRET=somesecret
-VISION_MODEL_PATH=models/.../model.h5
+MODEL_NAME=ModelGenerationName
+VISION_MODEL_PATH=models/.../vision_model.h5
 TAXONOMY_PATH=models/.../taxonomy.csv
 TF_GEO_MODEL_PATH=models/.../tf_gpmodel.h5
+ELEVATION_H3_R4_PATH=models/.../elevation_r4_5m.csv
+GEO_THRESHOLDS_PATH=models/.../thresholds.csv
+TAXON_RANGES_PATH=models/.../taxon_ranges
+GEO_MIN=0.005

requirements.txt

@@ -1,23 +1,24 @@
-scipy
-six
+flake8
+Flask
+Flask-WTF
+h3
+h3pandas
+itsdangerous
+jinja2
+keras
 matplotlib
 numpy
-tifffile
-umap_learn
 pandas
-torch
-Flask
 Pillow
-scikit_learn
-pyyaml
-Flask-WTF
+prison
 python-magic
-keras
-jinja2
-itsdangerous
+pyyaml
+scikit_learn
+scipy
+six
+tensorflow
+tifffile
+torch
+umap_learn
 werkzeug
 WTForms
-flake8
-h3
-h3pandas
-prison