update which notebooks are in this repo and gitignore/dockerignore, a…

…dd github workflow

.dockerignore

@@ -1,2 +1,21 @@
-maps
-test.ipynb
+# classification one inch
+worked_examples/geospatial/*classification_one_inch_maps/*
+!worked_examples/geospatial/*classification_one_inch_maps/Pipeline.ipynb
+!worked_examples/geospatial/*classification_one_inch_maps/annotations_one_inch/rail_space_#rw#.csv
+
+# text spotting one inch
+worked_examples/geospatial/text_spotting_one_inch_maps/*/*
+!worked_examples/geospatial/text_spotting_one_inch_maps/*/*/Pipeline.ipynb
+
+# classification mnist
+worked_examples/non-geospatial/classification_mnist/*
+!worked_examples/non-geospatial/classification_mnist/Pipeline.ipynb
+!worked_examples/non-geospatial/classification_mnist/annotations_mnist/mnist_#kasra#.csv
+!worked_examples/non-geospatial/classification_mnist/small_mnist/
+
+# classification plant phenotype
+worked_examples/non-geospatial/classification_plant_phenotype/*
+!worked_examples/non-geospatial/classification_plant_phenotype/Pipeline.ipynb
+!worked_examples/non-geospatial/classification_plant_phenotype/annotations_plant_phenotype_open_acess/phenotype_test_#kasra#.csv
+!worked_examples/non-geospatial/classification_plant_phenotype/dataset/
+

.github/workflows/check_notebooks.yml

@@ -0,0 +1,61 @@
+---
+    name: Test notebooks
+
+    on: 
+      push:
+        branches:
+          - dev
+      schedule:
+        - cron: 0 0 1 * *
+
+    # Run linter with github actions for quick feedbacks.
+    jobs:
+      all_tests:
+        runs-on: ubuntu-latest
+        steps:
+          - uses: actions/checkout@v2
+            with:
+              fetch-depth: 2
+
+          - name: Set up Python 3.11
+            uses: actions/setup-python@v2
+            with:
+              python-version: 3.11
+
+          - name: Update pip
+            run: |
+              python -m ensurepip
+              python -m pip install --upgrade pip
+    
+          - name: Install dependencies
+            run: |
+              python -m pip install wheel
+              python -m pip install numpy==1.26.4 torch==2.2.2 torchvision==0.17.2 -f https://download.pytorch.org/whl/torch_stable.html
+              python -m pip install "mapreader[dev]"
+              python -m pip install 'git+https://github.com/facebookresearch/detectron2.git'
+              python -m pip install 'git+https://github.com/maps-as-data/DeepSolo.git'
+              python -m pip install 'git+https://github.com/maps-as-data/DPText-DETR.git'
+              python -m pip install 'git+https://github.com/maps-as-data/MapTextPipeline.git'
+    
+          - name: Clone DPText-DETR
+            run: |
+              git clone https://github.com/maps-as-data/DPText-DETR.git
+    
+          - name: Clone DeepSolo
+            run: |
+              git clone https://github.com/maps-as-data/DeepSolo.git
+    
+          - name: Clone MapTextPipeline
+            run: |
+              git clone https://github.com/maps-as-data/MapTextPipeline.git
+    
+          - name: Hugging Face CLI
+            run: |
+              pip install -U "huggingface_hub[cli]"
+              huggingface-cli download rwood-97/DPText_DETR_ArT_R_50_poly art_final.pth --local-dir .
+              huggingface-cli download rwood-97/DeepSolo_ic15_res50 ic15_res50_finetune_synth-tt-mlt-13-15-textocr.pth --local-dir .
+              huggingface-cli download rwood-97/MapTextPipeline_rumsey rumsey-finetune.pth --local-dir .
+    
+          - name: Convert notebooks
+            run: |
+              find . -name "*.ipynb" -exec jupyter execute {} +

.gitignore

@@ -1,6 +1,21 @@
-maps
-test.ipynb
-parent_df.csv
-patch_df.csv
-.maps
-patches_*_pixel
+# classification one inch
+worked_examples/geospatial/*classification_one_inch_maps/*
+!worked_examples/geospatial/*classification_one_inch_maps/Pipeline.ipynb
+!worked_examples/geospatial/*classification_one_inch_maps/annotations_one_inch/rail_space_#rw#.csv
+
+# text spotting one inch
+worked_examples/geospatial/text_spotting_one_inch_maps/*/*
+!worked_examples/geospatial/text_spotting_one_inch_maps/*/*/Pipeline.ipynb
+
+# classification mnist
+worked_examples/non-geospatial/classification_mnist/*
+!worked_examples/non-geospatial/classification_mnist/Pipeline.ipynb
+!worked_examples/non-geospatial/classification_mnist/annotations_mnist/mnist_#kasra#.csv
+!worked_examples/non-geospatial/classification_mnist/small_mnist/
+
+# classification plant phenotype
+worked_examples/non-geospatial/classification_plant_phenotype/*
+!worked_examples/non-geospatial/classification_plant_phenotype/Pipeline.ipynb
+!worked_examples/non-geospatial/classification_plant_phenotype/annotations_plant_phenotype_open_acess/phenotype_test_#kasra#.csv
+!worked_examples/non-geospatial/classification_plant_phenotype/dataset/
+

Dockerfile

@@ -1,5 +1,5 @@
 # Use an official Python runtime as a parent image
-FROM python:3.9
+FROM python:3.11
 
 RUN apt-get update
 
@@ -12,10 +12,20 @@ WORKDIR /app
 COPY . /app
 
 # Install any needed packages specified in requirements.txt
-RUN pip install --no-cache-dir -r requirements.txt
-
-# Download all maps for example notebooks
-RUN python download-examples.py
+RUN python -m pip install --upgrade pip
+RUN python -m pip install numpy==1.26.4 torch==2.2.2 torchvision==0.17.2 -f https://download.pytorch.org/whl/torch_stable.html
+RUN python -m pip install --no-cache-dir -r requirements.txt
+
+# Clone text spotting repos
+RUN git clone https://github.com/maps-as-data/DPText-DETR.git
+RUN git clone https://github.com/maps-as-data/DeepSolo.git
+RUN git clone https://github.com/maps-as-data/MapTextPipeline.git
+
+# Get text spotting model weights
+RUN python -m pip install -U "huggingface_hub[cli]"
+RUN huggingface-cli download rwood-97/DPText_DETR_ArT_R_50_poly art_final.pth --local-dir .
+RUN huggingface-cli download rwood-97/DeepSolo_ic15_res50 ic15_res50_finetune_synth-tt-mlt-13-15-textocr.pth --local-dir .
+RUN huggingface-cli download rwood-97/MapTextPipeline_rumsey rumsey-finetune.pth --local-dir .
 
 # Make port 8888 available to the world outside this container
 EXPOSE 8888