Merge pull request #52 from nsidc/measures

Notebook to access, download and plot GeoTIFFs using MEaSUREs data sets as examples

.circleci/config.yml

@@ -14,6 +14,7 @@ jobs:
       - setup_remote_docker
       - run:
           name: Build and save Docker image
+          working_directory: ~/tutorials/binder
           command: |
             DOCKER_IMAGE=nsidc/tutorials
 
@@ -32,7 +33,7 @@ jobs:
             docker save -o build/saved-docker-image.tar ${DOCKER_IMAGE}:${TAG}
             echo "${DOCKER_IMAGE}:${TAG}" > build/docker-image-name.txt
       - persist_to_workspace:
-          root: ~/tutorials
+          root: ~/tutorials/binder
           paths:
             - build
 
@@ -41,7 +42,7 @@ jobs:
     steps:
       - setup_remote_docker
       - attach_workspace:
-          at: ~/tutorials
+          at: ~/tutorials/binder
       - deploy:
           name: Publish Docker image
           command: |

.github/workflows/scan_notebooks.py

@@ -26,9 +26,9 @@ def ensure_environment(notebook, libraries):
 
 def scan_notebook(notebook_path):
     notebook_path = notebook_path.replace(" ", "\\ ")
-    command = f"pipreqsnb {notebook_path} --print"
+    command = f"pipreqsnb {notebook_path} --print --debug"
 
-    libraries = []
+    libraries = set()
     p = subprocess.Popen(
         command,
         shell=True,
@@ -42,8 +42,10 @@ def scan_notebook(notebook_path):
         parsed_out = inline.decode("UTF-8").lower()
         if "==" in parsed_out:
             library = parsed_out.split("==")[0]
-            libraries.append(library)
-    print(libraries)
+            if library.lower() == "gdal":
+                library = "osgeo"
+            libraries.add(library)
+    print(list(libraries))
 
     ensure_environment(notebook_path, libraries)
 

.github/workflows/test.yml

@@ -1,72 +1,84 @@
 name: Test Notebooks
 
 on:
-  push:
   pull_request:
+    paths:
+      - notebooks/**
+      - binder/**
+      - '.github/workflows/'
     types: [opened, synchronize]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  posix:
-    name: Runtime (${{ matrix.os }}, Mambaforge)
+  linux:
+    name: Linux tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+    steps:
+      - uses: actions/checkout@v3
+      - name: "Install Conda environment with Micromamba"
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-env: true
+          environment-file: binder/conda-linux-64.lock
+          environment-name: nsidc-tutorials
+
+      - name: "Verify micromamba"
+        shell: bash -l {0}
+        run: |
+          micromamba info
+          jupyter kernelspec list
+          which python
+          conda list | sort
+
+      - name: "Verify that libraries used in notebooks are present in the environment"
+        shell: bash -l {0}
+        run: |
+          find notebooks -type f -iname \*.ipynb  -not -path '*\.ipynb_checkpoints/*' -not -path '*/iceflow/*'  | xargs -I % python .github/workflows/scan_notebooks.py -n %
+
+      - name: "Setup Quarto"
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          # version: 1.1.251
+          version: 1.3.361
+
+      - name: "Execute notebooks with Quarto"
+        env:
+          EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
+          EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}
+        shell: bash -l {0}
+        run: |
+          find notebooks -type f -name "*.ipynb" -not -path '*\.ipynb_checkpoints/*' -not -path '*endered*' -not -path '*SnowEx*'  | xargs -I F quarto render "F"  --execute-daemon-restart
+
+
+  win-osx:
+    name: Runtime (${{ matrix.os }}, micromamba)
     runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu", "macos"]
+        os: ["windows", "macos"]
         include:
-          - os: ubuntu
-            environment-file: binder/conda-linux-64.lock
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
+          - os: windows
+            environment-file: binder/conda-win-64.lock
           - os: macos
             environment-file: binder/conda-osx-64.lock
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - name: "Install Conda environment with Micromamba"
+        uses: mamba-org/setup-micromamba@v1
         with:
+          cache-env: true
           environment-file: ${{ matrix.environment-file }}
-          miniforge-variant: ${{ matrix.miniforge-variant }}
-          miniforge-version: ${{ matrix.miniforge-version }}
-          use-mamba: true
+          environment-name: nsidc-tutorials
 
-      - name: Bash
+      - name: "Verify micromamba"
         shell: bash -l {0}
         run: |
-          conda info
-          conda list
+          micromamba info
+          jupyter kernelspec list
           printenv | sort
-          find notebooks -type f -iname \*.ipynb  -not -path '*\.ipynb_checkpoints/*' -not -path "*/iceflow/*" | xargs -I % python .github/workflows/scan_notebooks.py -n %
-
-
-  # windows:
-  #   name: Runtime Windows Mambaforge
-  #   runs-on: windows-latest
-  #   strategy:
-  #     fail-fast: false
-  #   steps:
-  #     - uses: actions/checkout@v2
-  #     - uses: conda-incubator/setup-miniconda@v2
-  #       with:
-  #         environment-file: binder/conda-win-64.lock
-  #         miniforge-variant: Mambaforge
-  #         miniforge-version: latest
-  #         use-mamba: true
-
-  #     - name: PowerShell
-  #       shell: powershell
-  #       run: |
-  #         conda info
-  #         conda list
-
-  #     - name: PowerShell Core
-  #       shell: pwsh
-  #       run: |
-  #         conda info
-  #         conda list
-
-  #     - name: Cmd.exe
-  #       shell: cmd /C CALL {0}
-  #       run: >-
-  #         conda info && conda list

.gitignore

@@ -1,6 +1,7 @@
 MANIFEST
 notebook/Outputs
 build
+bin
 dist
 _build
 docs/man/*.gz

README.md

@@ -3,7 +3,7 @@
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/nsidc/NSIDC-Data-Tutorial/main?urlpath=lab/tree/notebooks)
 
-[![CircleCI](https://circleci.com/gh/nsidc/NSIDC-Data-Tutorials.svg?style=svg)](https://circleci.com/gh/nsidc/NSIDC-Data-Tutorials)
+[![Test Notebooks](https://github.com/nsidc/NSIDC-Data-Tutorials/actions/workflows/test.yml/badge.svg)](https://github.com/nsidc/NSIDC-Data-Tutorials/actions/workflows/test.yml)
 
 ## Summary
 
@@ -42,6 +42,17 @@ The notebooks on this project demonstrate how to search and access ITS_LIVE velo
 
 Originally presented to the UWG (User Working Group) in May 2022, this tutorial demonstrates how to search for ICESat-2 data hosted in the Earthdata Cloud and how to directly access it from an Amazon Web Services (AWS) Elastic Compute Cloud (EC2) instance using the `earthaccess` package.
 
+### [MEaSUREs](./notebooks/measures)
+
+**Download, crop, resample, and plot multiple GeoTIFFs**
+
+This tutorial guides you through programmatically accessing and downloading GeoTIFF files from the NSIDC DAAC to your local computer. We then crop and resample one GeoTIFF based on the extent and pixel size of another GeoTIFF, then plot one on top of the other. 
+
+We will use two data sets from the NASA [MEaSUREs](https://nsidc.org/data/measures) (Making Earth System data records for Use in Research Environments) program as an example:
+
+* [MEaSUREs Greenland Ice Mapping Project (GrIMP) Digital Elevation Model from GeoEye and WorldView Imagery, Version 2 (NSIDC-0715)](https://nsidc.org/data/nsidc-0715/versions/2)
+* [MEaSUREs Greenland Ice Velocity: Selected Glacier Site Velocity Maps from InSAR, Version 4 (NSIDC-0481)](https://nsidc.org/data/nsidc-0481/versions/4)
+
 ## Usage with Binder
 
 The Binder button above allows you to explore and run the notebook in a shared cloud computing environment without the need to install dependencies on your local machine. Note that this option will not directly download data to your computer; instead the data will be downloaded to the cloud environment.

binder/Dockerfile

@@ -0,0 +1,6 @@
+FROM pangeo/base-image:2023.01.13
+
+
+USER $NB_UID
+
+ENTRYPOINT ["jupyter", "lab","--ip=0.0.0.0","--allow-root"]