Merge branch 'main' into measures

.github/workflows/binder-badge.yml

@@ -0,0 +1,11 @@
+name: AddBinderBadge
+on:
+  pull_request_target:
+
+jobs:
+  badge:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: manics/action-binderbadge@main
+        with:
+          githubToken: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/scan_notebooks.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+
+import argparse
+import importlib
+import subprocess
+import sys
+
+
+def ensure_environment(notebook, libraries):
+    for lib_name in libraries:
+        try:
+            importlib.import_module(lib_name)
+
+        except Exception:
+            try:
+
+                importlib.import_module(lib_name, f".{lib_name}")
+            except ModuleNotFoundError or ImportError as ee:
+
+                print(
+                    f"{notebook} uses a library that is not present in the current environment: {ee.msg}",
+                    file=sys.stderr,
+                )
+                exit(1)
+
+
+def scan_notebook(notebook_path):
+    notebook_path = notebook_path.replace(" ", "\\ ")
+    command = f"pipreqsnb {notebook_path} --print"
+
+    libraries = []
+    p = subprocess.Popen(
+        command,
+        shell=True,
+        stdout=subprocess.PIPE,
+    )
+
+    while True:
+        inline = p.stdout.readline()
+        if not inline:
+            break
+        parsed_out = inline.decode("UTF-8").lower()
+        if "==" in parsed_out:
+            library = parsed_out.split("==")[0]
+            libraries.append(library)
+    print(libraries)
+
+    ensure_environment(notebook_path, libraries)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-n", "--notebook", help="<Required> Set flag", required=True)
+    args = parser.parse_args()
+    scan_notebook(args.notebook)

.github/workflows/test.yml

@@ -0,0 +1,72 @@
+name: Test Notebooks
+
+on:
+  push:
+  pull_request:
+    types: [opened, synchronize]
+
+jobs:
+  posix:
+    name: Runtime (${{ matrix.os }}, Mambaforge)
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu", "macos"]
+        include:
+          - os: ubuntu
+            environment-file: binder/conda-linux-64.lock
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+          - 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
+        with:
+          environment-file: ${{ matrix.environment-file }}
+          miniforge-variant: ${{ matrix.miniforge-variant }}
+          miniforge-version: ${{ matrix.miniforge-version }}
+          use-mamba: true
+
+      - name: Bash
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda 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

@@ -18,6 +18,7 @@ notebook/static/*/js/main.min.js*
 notebook/static/lab/*bundle.js
 notebooks/itslive/data/*.nc
 notebooks/iceflow/data
+notebooks/*/Outputs
 .python-version
 node_modules
 *.py[co]

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

Dockerfile

@@ -1,24 +1,22 @@
-FROM jupyter/base-notebook:latest
+FROM jupyter/base-notebook:2022-02-17
 
 USER root
 
 # Install all OS dependencies for notebook server that starts but lacks all
 # features (e.g., download as all possible file formats)
 ENV DEBIAN_FRONTEND noninteractive
 RUN apt-get update \
- && apt-get install -yq --no-install-recommends git \
+ && apt-get install -yq --no-install-recommends git jq \
  && apt-get clean  && apt autoremove && rm -rf /var/lib/apt
 
 USER $NB_UID
 
 ADD binder/environment.yml $HOME
-ADD binder/postBuild $HOME
-RUN conda env update -f environment.yml -n base && conda clean --force --yes --all  && rm $HOME/environment.yml && \
+RUN mamba env update -f environment.yml -n base && conda clean --force --yes --all  && rm $HOME/environment.yml && \
 npm cache clean --force && \
-rm -rf /opt/conda/lib/python3.7/site-packages/awscli/examples \
+rm -rf /opt/conda/lib/python3.9/site-packages/awscli/examples \
 && find /opt/conda/ -follow -type f -name '*.a' -delete \
 && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
-&& fix-permissions /home/$NB_USER && fix-permissions $HOME \
-&& ./postBuild
+&& fix-permissions /home/$NB_USER && fix-permissions
 
 ENTRYPOINT ["jupyter", "lab","--ip=0.0.0.0","--allow-root"]

README.md

@@ -7,7 +7,7 @@
 
 ## Summary
 
-This combined repository includes tutorials and code resources provided by the NASA National Snow and Ice Data Center Distributed Active Archive Center (NSIDC DAAC). These tutorials are provided as Python-based Jupyter notebooks that provide guidance on working with various data products, including how to access, subset, transform, and visualize data. Each tutorial can be accessed by navigating to the /notebooks folder of this repository. Please see the README files associated with each individual tutorial folder for more information on each tutorial and their learning objectives.
+This combined repository includes tutorials and code resources provided by the NASA National Snow and Ice Data Center Distributed Active Archive Center (NSIDC DAAC). These tutorials are provided as Python-based Jupyter notebooks that provide guidance on working with various data products, including how to access, subset, transform, and visualize data. Each tutorial can be accessed by navigating to the /notebooks folder of this repository. Please see the README files associated with each individual tutorial folder for more information on each tutorial and their learning objectives. Please note that all branches outside of `Main` should be considered in development and are not supported. 
 
 ## Tutorials
 
@@ -36,6 +36,12 @@ The Inter-mission Time Series of Land Ice Velocity and Elevation (ITS_LIVE) proj
 
 The notebooks on this project demonstrate how to search and access ITS_LIVE velocity pairs and provide a simple example on how to build a data cube.
 
+### [ICESat-2_Cloud_Access](./notebooks/ICESat-2_Cloud_Access)
+
+**Accessing and working with ICESat-2 Data in the Cloud**
+
+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.
+
 ## 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.
@@ -143,33 +149,39 @@ If you started your container with the `-d`/`--detach` option, check `docker log
 
 8. You can now interact with the notebooks to explore and access data.
 
-## Usage with Conda
+## Usage with Mamba/Conda
 
-Install miniconda3 (Python 3.7) for your platform from [https://docs.conda.io/en/latest/miniconda.html](https://docs.conda.io/en/latest/miniconda.html)
+> Note: If we already have conda or mamba installed we can skip the first step.
 
-Download the [NSIDC-Data-Tutorials](https://github.com/nsidc/NSIDC-Data-Tutorials) repository from Github by clicking the green 'Code' button located at the top right of the repository page and clicking 'Download Zip'.
+1. Install mambaforge (Python 3.9+) for your platform from [mamba documentation](https://mamba.readthedocs.io/en/latest/installation.html)
 
-Unzip the file, and open a command line or terminal window in the NSIDC-Data-Tutorials folder's location.
 
-From a command line or terminal window, install the required environment with the following commands:
+2. Download the [NSIDC-Data-Tutorials](https://github.com/nsidc/NSIDC-Data-Tutorials) repository from Github by clicking the green 'Code' button located at the top right of the repository page and clicking 'Download Zip'. Unzip the file, and open a command line or terminal window in the NSIDC-Data-Tutorials folder's location. 
 
+3. From a command line or terminal window, install the required environment with the following commands:
+
+Linux 
 ```bash
-conda env create -f binder/environment.yml && conda activate tutorials
-./binder/postBuild
+mamba create -n nsidc-tutorials --file binder/conda-linux-64.lock
 ```
 
-You should now see that the dependencies were installed and our environment is ready to be used.
-
-If you are a returning user, please make sure your repository is up to date and run the following to update your environment:
-
+OSX
+```bash
+mamba create -n nsidc-tutorials --file binder/conda-osx-64.lock
 ```
-conda env update -f binder/environment.yml
+
+Windows 
+```bash
+mamba create -n nsidc-tutorials --file binder/conda-win-64.lock
 ```
 
+You should now see that the dependencies were installed and our environment is ready to be used.
+
+
 Activate the environment with
 
 ```
-conda activate tutorials
+conda activate nsidc-tutorials
 ```
 
 Launch the notebook locally with the following command:
@@ -180,6 +192,20 @@ jupyter lab
 
 This should open a browser window with the JupyterLab IDE, showing your current working directory on the left-hand navigation. Navigate to the tutorial folder of choice and click on their associated *.ipynb files to get started.
 
+
+### Tutorial Environments
+
+Although the nsidc-tutorial environment should run all the notebooks in this repository, we also include tutorial-specific environments that will only contain the dependencies for them. If we don't want to "pollute" our conda environments and we are only going to work with one of the tutorials we recommend to use them instead of the `nsidc-tutorial` environment. The steps to install them are exactly the same but the environment files are inside the environment folders in each of the tutorials. e.g. for ITS_LIVE
+
+```bash
+cd notebooks/itslive 
+mamba create -n nsidc-itslive --file environment/conda-linux-64.lock
+conda activate nsidc-itslive
+jupyter lab
+```
+
+This should create a pinned environment that should be fully reproducible across platforms.
+
 > **NOTE:** Sometimes Conda environments change (break) even with pinned down dependencies. If you run into an issue with dependencies for the tutorials please open an issue and we'll try to fix it as soon as possible.
 
 

binder/apt.txt

@@ -1 +1,11 @@
+curl
+git
+jq
+htop
+tmux
+tree
+vim
 neovim
+net-tools
+iproute2
+ffmpeg