remove binder (#50)

Author: e-marshall

book/_config.yml

@@ -32,11 +32,10 @@ bibtex_bibfiles:
 # Information about where the book exists on the web
 repository:
   url: https://github.com/e-marshall/cloud-open-source-geospatial-datacube-workflows
-  #url: https://e-marshall.github.io/cloud-open-source-geospatial-datacube-workflows/introduction.html  # Online location of your book
-  branch: main  # Which branch of the repository should be used when creating links (optional)
+  branch: main  
 
 launch_buttons:
-  binderhub_url: "https://mybinder.org"
+  #binderhub_url: "https://mybinder.org"
   notebook_interface: "jupyterlab"
 
 # Add GitHub buttons to your book

book/background/5_software.md

@@ -28,7 +28,7 @@ Note that the first `pixi run` will download specific versions of all required P
 ```cd cloud-open-source-geospatial-datacube-workflows/book```
 
 3. Create and activate a conda environment from the `environment.yml` file located in the repo:  
-```conda env create -f .binder/environment.yml```
+```conda env create -f environment.yml```
 
 4. Start Jupyterlab and navigate to the directories containing the Jupyter notebooks (`itslive/nbs` and `s1/nbs`):  
 ```jupyterlab```

book/background/software.md

@@ -28,7 +28,7 @@ Note that the first `pixi run` will download specific versions of all required P
 ```cd cloud-open-source-geospatial-datacube-workflows/book```
 
 3. Create and activate a conda environment from the `environment.yml` file located in the repo:  
-```conda env create -f .binder/environment.yml```
+```conda env create -f environment.yml```
 
 4. Start Jupyterlab and navigate to the directories containing the Jupyter notebooks (`itslive/nbs` and `s1/nbs`):  
 ```jupyterlab```
@@ -38,7 +38,7 @@ Both tutorials use functions that are stored in scripts associated with each dat
 
 ## *Running tutorial materials on a hosted JupyterHub*
 
-Many NASA datasets including ITS_LIVE are hosted in the AWS us-west-2 data center. While these tutorial notebooks are designed to be run on any computer, if you intend to modify the notebooks and access data directly it is desireable to run computations in the same data center. A convenient way access a computer in AWS us-west-2 is to use a hosted JupyterHub platform such as one of the following:
+Many NASA datasets including ITS_LIVE are hosted in the AWS us-west-2 data center. While these tutorial notebooks are designed to be run on any computer, if you intend to modify the notebooks and access data directly it is desirable to run computations in the same data center. A convenient way access a computer in AWS us-west-2 is to use a hosted JupyterHub platform such as one of the following:
 
 - https://docs.openveda.cloud/user-guide/scientific-computing/
 - https://opensarlab-docs.asf.alaska.edu

book/book_refs.bib

@@ -542,16 +542,17 @@ @article{wilkinsonFAIRGuidingPrinciples2016
   doi = {10.1038/sdata.2016.18},
   abstract = {There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders---representing academia, industry, funding agencies, and scholarly publishers---have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.}
 }
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% DATA %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 @misc{Gardner_Scambos_2022, 
     title={MEaSUREs ITS_LIVE Landsat Image-Pair Glacier and Ice Sheet Surface Velocities, Version 1}, 
-    url={https://nsidc.org/data/NSIDC-0775/versions/1}, DOI={10.5067/IMR9D3PEI28U}, 
+    url={https://nsidc.org/data/NSIDC-0775/versions/1}, 
+    DOI={10.5067/IMR9D3PEI28U}, 
     publisher={NASA National Snow and Ice Data Center Distributed Active Archive Center}, 
-    author={Gardner, A., M. Fahnestock and Scambos, T.}, year={2022} 
+    author={Gardner, A., M. Fahnestock and Scambos, T.}, 
+    year={2022} 
 }
 
- @misc{RGI_Consortium_2023, 
+@misc{RGI_Consortium_2023, 
     title={Randolph Glacier Inventory - A Dataset of Global Glacier Outlines, Version 7}, 
     url={https://nsidc.org/data/NSIDC-0770/versions/7}, 
     DOI={10.5067/F6JMOVY5NAVZ}, 
@@ -564,7 +565,6 @@ @misc{ASF_Sentinel1
     url={https://hyp3-docs.asf.alaska.edu/guides/rtc_product_guide/},
     publisher={Alaska Satellite Facility Distributed Active Archive Center},
     year={2023},
-    
 }
 
 @misc{hogenson_2024_10903242,
@@ -674,55 +674,47 @@ @Article{         harris2020array
  url           = {https://doi.org/10.1038/s41586-020-2649-2}
 }
 
- @misc{matplotlib_2021, 
-        title={matplotlib/matplotlib: REL: v3.5.1}, 
-        url={https://doi.org/10.5281/zenodo.5773480}, 
-        DOI={10.5281/zenodo.5773480}, 
-        publisher={Zenodo}, 
-        author={Caswell, Thomas A. and Droettboom, Michael and Lee, Antony and Andrade, Elliott Sales de and Hoffmann, Tim and Hunter, John and Klymak, Jody and Firing, Eric and Stansby, David and Varoquaux, Nelle and Nielsen, Jens Hedegaard and Root, Benjamin and May, Ryan and Elson, Phil and Seppänen, Jouni K. and Dale, Darren and Lee, Jae-Joon and McDougall, Damon and Straw, Andrew and Hobson, Paul and hannah and Gohlke, Christoph and Vincent, Adrien F. and Yu, Tony S. and Ma, Eric and Silvester, Steven and Moad, Charlie and Kniazev, Nikita and Ernest, Elan and Ivanov, Paul}, 
-        year={2021}, month=dec }
-        
-
- @misc{JupyterBookCommunity_2021, 
-        title={Jupyter Book}, 
-        url={https://doi.org/10.5281/zenodo.4539666}, 
-        DOI={10.5281/zenodo.4539666}, 
-        publisher={Zenodo}, 
-        author={Executable Books Community}, 
-        year={2021}, month=feb }
-
- @misc{Gillies_van_der_Wel_Van_den_Bossche_Taves_Arnott_Ward_others_2022, 
-        title={Shapely}, 
-        url={https://doi.org/10.5281/zenodo.7428463}, 
-        DOI={10.5281/zenodo.7428463}, 
-        publisher={Zenodo}, 
-        author={Gillies, Sean and van der Wel, Casper and Van den Bossche, Joris and Taves, Mike W. and Arnott, Joshua and Ward, Brendan C. and others}, 
-        year={2022}, month=dec }
-
- @article{Hoyer_Hamman_2017, 
-        title={xarray: N-D labeled Arrays and Datasets in Python}, 
-        volume={5}, 
-        ISSN={2049-9647}, 
-        url={https://openresearchsoftware.metajnl.com/article/10.5334/jors.148/}, 
-        DOI={10.5334/jors.148}, number={1}, 
-        journal={Journal of Open Research Software}, 
-        author={Hoyer, Stephan and Hamman, Joe}, 
-        year={2017}, month=apr, pages={10}, language={en} }
-
- @misc{Jordahl_Bossche_Fleischmann_McBride_Wasserman_Badaracco_Gerard_Snow_Tratner_Perry_etal_2021, 
-        title={geopandas/geopandas: v0.10.0}, 
-        url={https://doi.org/10.5281/zenodo.5546558}, 
-        DOI={10.5281/zenodo.5546558}, 
-        publisher={Zenodo}, 
-        author={Jordahl, Kelsey and Bossche, Joris Van den and Fleischmann, Martin and McBride, James and Wasserman, Jacob and Badaracco, Adrian Garcia and Gerard, Jeffrey and Snow, Alan D. and Tratner, Jeff and Perry, Matthew and Farmer, Carson and Hjelle, Geir Arne and Cochran, Micah and Gillies, Sean and Culbertson, Lucas and Bartos, Matt and Ward, Brendan and Caria, Giacomo and Taves, Mike and Eubank, Nick and sangarshanan and Flavin, John and Richards, Matt and Rey, Sergio and maxalbert and Bilogur, Aleksey and Ren, Christopher and Arribas-Bel, Dani and Mesejo-León, Daniel and Wasser, Leah}, 
-        year={2021}, month=oct }
- @inproceedings{Jupyter_Bussonnier_Forde_Freeman_Granger_Head_Holdgraf_Kelley_Nalvarte_Osheroff_etal_2018, 
-        address={Austin, Texas}, 
-        title={Binder 2.0 - Reproducible, interactive, sharable environments for science at scale}, 
-        url={https://conference.scipy.org/proceedings/scipy2018/project_jupyter.html}, 
-        DOI={10.25080/Majora-4af1f417-011},
-        author={Jupyter, Project and Bussonnier, Matthias and Forde, Jessica and Freeman, Jeremy and Granger, Brian and Head, Tim and Holdgraf, Chris and Kelley, Kyle and Nalvarte, Gladys and Osheroff, Andrew and Pacer, M and Panda, Yuvi and Perez, Fernando and Ragan-Kelley, Benjamin and Willing, Carol},
-        year={2018}, pages={113–120}, language={en} }
+@misc{matplotlib_2021, 
+      title={matplotlib/matplotlib: REL: v3.5.1}, 
+      url={https://doi.org/10.5281/zenodo.5773480}, 
+      DOI={10.5281/zenodo.5773480}, 
+      publisher={Zenodo}, 
+      author={Caswell, Thomas A. and Droettboom, Michael and Lee, Antony and Andrade, Elliott Sales de and Hoffmann, Tim and Hunter, John and Klymak, Jody and Firing, Eric and Stansby, David and Varoquaux, Nelle and Nielsen, Jens Hedegaard and Root, Benjamin and May, Ryan and Elson, Phil and Seppänen, Jouni K. and Dale, Darren and Lee, Jae-Joon and McDougall, Damon and Straw, Andrew and Hobson, Paul and hannah and Gohlke, Christoph and Vincent, Adrien F. and Yu, Tony S. and Ma, Eric and Silvester, Steven and Moad, Charlie and Kniazev, Nikita and Ernest, Elan and Ivanov, Paul}, 
+      year={2021}, month=dec } 
+
+@misc{JupyterBookCommunity_2021, 
+      title={Jupyter Book}, 
+      url={https://doi.org/10.5281/zenodo.4539666}, 
+      DOI={10.5281/zenodo.4539666}, 
+      publisher={Zenodo}, 
+      author={Executable Books Community}, 
+      year={2021}, month=feb }
+
+@misc{Gillies_van_der_Wel_Van_den_Bossche_Taves_Arnott_Ward_others_2022, 
+      title={Shapely}, 
+      url={https://doi.org/10.5281/zenodo.7428463}, 
+      DOI={10.5281/zenodo.7428463}, 
+      publisher={Zenodo}, 
+      author={Gillies, Sean and van der Wel, Casper and Van den Bossche, Joris and Taves, Mike W. and Arnott, Joshua and Ward, Brendan C. and others}, 
+      year={2022}, month=dec }
+
+@article{Hoyer_Hamman_2017, 
+      title={xarray: N-D labeled Arrays and Datasets in Python}, 
+      volume={5}, 
+      ISSN={2049-9647}, 
+      url={https://openresearchsoftware.metajnl.com/article/10.5334/jors.148/}, 
+      DOI={10.5334/jors.148}, number={1}, 
+      journal={Journal of Open Research Software}, 
+      author={Hoyer, Stephan and Hamman, Joe}, 
+      year={2017}, month=apr, pages={10}, language={en} }
+
+@misc{Jordahl_Bossche_Fleischmann_McBride_Wasserman_Badaracco_Gerard_Snow_Tratner_Perry_etal_2021, 
+      title={geopandas/geopandas: v0.10.0}, 
+      url={https://doi.org/10.5281/zenodo.5546558}, 
+      DOI={10.5281/zenodo.5546558}, 
+      publisher={Zenodo}, 
+      author={Jordahl, Kelsey and Bossche, Joris Van den and Fleischmann, Martin and McBride, James and Wasserman, Jacob and Badaracco, Adrian Garcia and Gerard, Jeffrey and Snow, Alan D. and Tratner, Jeff and Perry, Matthew and Farmer, Carson and Hjelle, Geir Arne and Cochran, Micah and Gillies, Sean and Culbertson, Lucas and Bartos, Matt and Ward, Brendan and Caria, Giacomo and Taves, Mike and Eubank, Nick and sangarshanan and Flavin, John and Richards, Matt and Rey, Sergio and maxalbert and Bilogur, Aleksey and Ren, Christopher and Arribas-Bel, Dani and Mesejo-León, Daniel and Wasser, Leah}, 
+      year={2021}, month=oct }
 
 @misc{philipp_rudiger_2020_holoviz,
   title = {Holoviz/Hvplot: {{Version}} 0.5.2},
@@ -742,38 +734,38 @@ @misc{cherian_2025_cfxarray
   swhid = {swh:1:dir:2677bf2878ee050d08d4ebb7e118e2806333f368 ;origin=https://doi.org/10.5281/zenodo.4749735;vis it=swh:1:snp:0385c9420b2e660dc18ce9cd5255579a8e5f0 e52;anchor=swh:1:rel:212af174c9fd0b2be3fd213115f78 42111692df1;path=xarray-contrib-cf-xarray-760b6b0}
 }
 
- @misc{Zarr_2020_dev, 
-        title={zarr-developers/zarr-python: v2.4.0}, 
-        url={https://doi.org/10.5281/zenodo.3773450}, 
-        DOI={10.5281/zenodo.3773450}, publisher={Zenodo}, 
-        author={Miles, Alistair and Kirkham, John and Durant, Martin and Bourbeau, James and Onalan, Tarik and Hamman, Joe and Patel, Zain and shikharsg and Rocklin, Matthew and dussin, raphael and Schut, Vincent and Andrade, Elliott Sales de and Abernathey, Ryan and Noyes, Charles and sbalmer and bot, pyup io and Tran, Tommy and Saalfeld, Stephan and Swaney, Justin and Moore, Josh and Jevnik, Joe and Kelleher, Jerome and Funke, Jan and Sakkis, George and Barnes, Chris and Banihirwe, Anderson}, 
-        year={2020}, month=apr }
- @misc{rioxarray_2022_dev, 
-        title={corteva/rioxarray: 0.12.1}, 
-        url={https://doi.org/10.5281/zenodo.7080195}, 
-        DOI={10.5281/zenodo.7080195}, 
-        publisher={Zenodo}, 
-        author={Snow, Alan D. and Brochart, David and Raspaud, Martin and Taves, Mike and Bell, Ray and RichardScottOZ and Chegini, Taher and Amici, Alessandro and Braun, Rémi and Annex, Andrew and Brandt, Carlos H. and Hoese, David and Bunt, Fred and GBallesteros and Scheick, Jessica and Hamman, Joe and jonasViehweger and Zehner, Markus and Cordeiro, Mauricio and Henderson, Scott and Miller, Seth and Badger, The Gitter and Augspurger, Tom and apiwat-chantawibul and pmallas}, 
-        year={2022}, month=sep }
- @misc{Source_McFarland_Emanuele_Morris_Augspurger_2022, 
-        title={microsoft/PlanetaryComputer: October 2022}, 
-        url={https://doi.org/10.5281/zenodo.7261897},
-        DOI={10.5281/zenodo.7261897}, 
-        publisher={Zenodo}, 
-        author={Source, Microsoft Open and McFarland, Matt and Emanuele, Rob and Morris, Dan and Augspurger, Tom}, 
-        year={2022}, month=oct }
- @misc{Pandasteam_2024, 
-        title={pandas-dev/pandas: Pandas}, 
-        url={https://doi.org/10.5281/zenodo.10537285}, 
-        DOI={10.5281/zenodo.10537285},
-        publisher={Zenodo}, 
-        author={team, The pandas development}, 
-        year={2024}, month=jan }
- @Manual{DaskLibrary,
-          title = {Dask: Library for dynamic task scheduling},
-          author = {{Dask Development Team}},
-          year = {2016},
-          url = {http://dask.pydata.org},
+@misc{Zarr_2020_dev, 
+      title={zarr-developers/zarr-python: v2.4.0}, 
+      url={https://doi.org/10.5281/zenodo.3773450}, 
+      DOI={10.5281/zenodo.3773450}, publisher={Zenodo}, 
+      author={Miles, Alistair and Kirkham, John and Durant, Martin and Bourbeau, James and Onalan, Tarik and Hamman, Joe and Patel, Zain and shikharsg and Rocklin, Matthew and dussin, raphael and Schut, Vincent and Andrade, Elliott Sales de and Abernathey, Ryan and Noyes, Charles and sbalmer and bot, pyup io and Tran, Tommy and Saalfeld, Stephan and Swaney, Justin and Moore, Josh and Jevnik, Joe and Kelleher, Jerome and Funke, Jan and Sakkis, George and Barnes, Chris and Banihirwe, Anderson}, 
+      year={2020}, month=apr }
+@misc{rioxarray_2022_dev, 
+      title={corteva/rioxarray: 0.12.1}, 
+      url={https://doi.org/10.5281/zenodo.7080195}, 
+      DOI={10.5281/zenodo.7080195}, 
+      publisher={Zenodo}, 
+      author={Snow, Alan D. and Brochart, David and Raspaud, Martin and Taves, Mike and Bell, Ray and RichardScottOZ and Chegini, Taher and Amici, Alessandro and Braun, Rémi and Annex, Andrew and Brandt, Carlos H. and Hoese, David and Bunt, Fred and GBallesteros and Scheick, Jessica and Hamman, Joe and jonasViehweger and Zehner, Markus and Cordeiro, Mauricio and Henderson, Scott and Miller, Seth and Badger, The Gitter and Augspurger, Tom and apiwat-chantawibul and pmallas}, 
+      year={2022}, month=sep }
+@misc{Source_McFarland_Emanuele_Morris_Augspurger_2022, 
+      title={microsoft/PlanetaryComputer: October 2022}, 
+      url={https://doi.org/10.5281/zenodo.7261897},
+      DOI={10.5281/zenodo.7261897}, 
+      publisher={Zenodo}, 
+      author={Source, Microsoft Open and McFarland, Matt and Emanuele, Rob and Morris, Dan and Augspurger, Tom}, 
+      year={2022}, month=oct }
+@misc{Pandasteam_2024, 
+      title={pandas-dev/pandas: Pandas}, 
+      url={https://doi.org/10.5281/zenodo.10537285}, 
+      DOI={10.5281/zenodo.10537285},
+      publisher={Zenodo}, 
+      author={team, The pandas development}, 
+      year={2024}, month=jan }
+@Manual{DaskLibrary,
+        title = {Dask: Library for dynamic task scheduling},
+        author = {{Dask Development Team}},
+        year = {2016},
+        url = {http://dask.pydata.org},
 }
 
 

.binder/book_linux-64_conda_spec.txt renamed to book_linux-64_conda_spec.txt

@@ -352,13 +352,6 @@ @misc{Jordahl_Bossche_Fleischmann_McBride_Wasserman_Badaracco_Gerard_Snow_Tratne
         publisher={Zenodo}, 
         author={Jordahl, Kelsey and Bossche, Joris Van den and Fleischmann, Martin and McBride, James and Wasserman, Jacob and Badaracco, Adrian Garcia and Gerard, Jeffrey and Snow, Alan D. and Tratner, Jeff and Perry, Matthew and Farmer, Carson and Hjelle, Geir Arne and Cochran, Micah and Gillies, Sean and Culbertson, Lucas and Bartos, Matt and Ward, Brendan and Caria, Giacomo and Taves, Mike and Eubank, Nick and sangarshanan and Flavin, John and Richards, Matt and Rey, Sergio and maxalbert and Bilogur, Aleksey and Ren, Christopher and Arribas-Bel, Dani and Mesejo-León, Daniel and Wasser, Leah}, 
         year={2021}, month=oct }
- @inproceedings{Jupyter_Bussonnier_Forde_Freeman_Granger_Head_Holdgraf_Kelley_Nalvarte_Osheroff_etal_2018, 
-        address={Austin, Texas}, 
-        title={Binder 2.0 - Reproducible, interactive, sharable environments for science at scale}, 
-        url={https://conference.scipy.org/proceedings/scipy2018/project_jupyter.html}, 
-        DOI={10.25080/Majora-4af1f417-011},
-        author={Jupyter, Project and Bussonnier, Matthias and Forde, Jessica and Freeman, Jeremy and Granger, Brian and Head, Tim and Holdgraf, Chris and Kelley, Kyle and Nalvarte, Gladys and Osheroff, Andrew and Pacer, M and Panda, Yuvi and Perez, Fernando and Ragan-Kelley, Benjamin and Willing, Carol},
-        year={2018}, pages={113–120}, language={en} }
 
  @misc{Miles_Kirkham_Durant_Bourbeau_Onalan_Hamman_Patel_shikharsg_Rocklin_dussin_etal_2020, 
         title={zarr-developers/zarr-python: v2.4.0},