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Bugfix/sof 5578 wip - Make Colab Great Again #71

Merged
merged 90 commits into from
Jun 21, 2023
Merged

Bugfix/sof 5578 wip - Make Colab Great Again #71

merged 90 commits into from
Jun 21, 2023

Commits on Jun 13, 2023

  1. Update notebooks to load the remote code in a more IPython friendly m… 

    …anner
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  2. Do not clone repo via examples/utils/initialize_settings.py

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  3. Ease pins in requirements-colab.txt

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  4. CLN: do not bother with condacolab

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  5. Update steps in the auth notebook

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  6. Fix colab URL in the auth notebook

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  7. BLD: Reduce the number of requirements and use concrete requirements

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  8. BLD: pymatgen 2023.5.31

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  9. Temp install of api-client from GH

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  10. pandas v1.5.3

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  11. Use released exabyte-api-client

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  12. Convert more notebooks to the new approach

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  13. Fix a link to Google Colab in `import_materials_from_materialsproject… 

    ….ipynb`
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  14. get_authentication_params.ipynb: change to the parent dir before ru… 

    …nning imports
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  15. REF: refactor how we get the env in Colab

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  16. Update the auth notebook to use a single script to set up the env

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  17. Move settings.* to utils/ and update setup.py with the respecti… 

    …ve json file
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  18. Fix imports for settings as a part of a package

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  19. CLN: stripout notebooks (auth and import from MP)

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  20. REF: better prioritization of the env vars vs. JSON input

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  21. ENH: allow to rerun the env.sh script without failures

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  22. CLN: clean up debug prints and make the cells consistent

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  23. DOC: fix the link to settings.json

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  24. Update the branch name for notebooks

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  25. CLN: silence the output of curl and init bash script in notebooks cells

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  26. CLN: rename references to the repo from exabyte-api-examples -> `ex… 

    …abyte-api-examples`
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  27. CLN: stripout outputs from material/get_materials_by_formula.ipynb

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Commits on Jun 14, 2023

  1. Enable running with a local Jupyter instance

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  2. MNT: tweak verbosity conditions

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Commits on Jun 15, 2023

  1. FIX: examples/workflow/get_workflows.ipynb

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  2. FIX: examples/material/create_material.ipynb

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  3. ENH: enable git-lfs support for some notebooks

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  4. FIX: examples/material/import_materials_from_poscar.ipynb

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  5. MNT: do not execute code on import from initialize_settings.py

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  6. ENH: silence apt/git commands output from env.sh

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  7. ENH: entry point to return the notebook path only

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  8. MNT: rearrange env.sh script

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  9. FIX: return -> print in the cli() func

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  10. MNT: back to return, but clean up another stray print

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  11. FIX: print, not return for the entry point

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  12. FIX: parens, not curly braces for shell cmd execution

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  13. ENH: better output of the ready env

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  14. ENH: export notebook dir from the env.sh script

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  15. MNT: change to dir in cells only works with Python (%cd ..., `os.ch… 

    …dir(...)`), not bash (`!cd ...`)
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  16. CLN: stripout output from `examples/material/import_materials_from_po… 

    …scar.ipynb`
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  17. FIX: examples/job/create_and_submit_job.ipynb

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  18. ENH: minor print improvement

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  19. FIX: examples/job/get-file-from-job.ipynb (updated initialization a… 

    …nd stripout output)
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  20. FIX: add a missing import of urllib in `examples/job/get-file-from-… 

    …job.ipynb`
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  21. FIX: examples/job/run-simulations-and-extract-properties.ipynb (upd… 

    …ated initialization and stripout output)
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  22. FIX: examples/job/ml-train-model-predict-properties.ipynb (updated … 

    …initialization and stripout output)
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  23. DOC: update instructions to also install utils in the dev mode (so th… 

    …at `settings.json` file is picked up correctly)
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  24. DOC: fix references to settings.json

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  25. MNT: better handling of Colab vs. local Jupyter

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Commits on Jun 16, 2023

  1. MNT: address review comments (env vars names, descriptions, etc.)

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  2. MNT: fix typo in username placeholder

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  3. FIX: correct entry point notebook-path

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  4. DEV: add a convenience script to update branch names in the notebooks

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  5. MNT: dev -> bugfix/SOF-5578-WIP branches in Colab URLs

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  6. PKG: move setup.py to the root of the repo and make corresponding a… 

    …djustments to the code
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  7. MNT: docs.exabyte.io -> docs.mat3ra.com

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  8. FIX: fix examples imports in the notebooks

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  9. FIX: fix imports

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  10. MNT: platform.exabyte.io -> platform.mat3ra.com

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  11. FIX: fix import of settings in utils/generic.py

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  12. FIX: install api-examples in a non-editable mode

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  13. MNT: absolute import of settings

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Commits on Jun 17, 2023

  1. ENH: add a helper script to render Jupyter notebook files (.ipynb) 

    The workflow is as follows:
- parse the README.md file and extract all the notebooks listed in the table;
- for each notebook:
  - execute `nbstripout` to strip output cells;
  - execute `nbconvert` to populate the .ipynb file in place;
  - execute `nbconvert` to .py.
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  2. MNT: ignore generated artifacts after notebooks runs

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  3. FIX: use BANK_WORKFLOW_ID="56xDyXsPMNJ7cF9nv" for run-simulations-a… 

    …nd-extract-properties.ipynb
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  4. DOC: update the reference to the bank id in the text cell of run-simu… 

    …lations-and-extract-properties.ipynb
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  5. MNT: configure the rendering script to ignore run-simulations-and-ext… 

    …ract-properties.ipynb
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  6. [AUTO] automatically updated notebooks with the rendering script

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Commits on Jun 19, 2023

  1. FIX: update references from Exabyte/.io -> Mat3ra/.com per PR review 

    - get-file-from-job.*
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  2. FIX: update references from Exabyte/.io -> Mat3ra/.com per PR review 

    - ml-train-model-predict-properties.*
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  3. FIX: update references from Exabyte/.io -> Mat3ra/.com per PR review 

    - get_authentication_params.*
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  4. FIX: address review comments regarding the names and docstrings in `i… 

    …nitialize_settings.py`
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  5. FIX: update references from Exabyte/.io -> Mat3ra/.com per PR review 

    Update the other files which weren't mentioned in the PR review:

- README.md
- examples/job/create_and_submit_job.*
- examples/job/run-simulations-and-extract-properties.*
- examples/material/api_interoperability_showcase.*
- examples/material/create_material.*
- examples/material/get_materials_by_formula.*
- examples/material/import_materials_from_materialsproject.*
- examples/material/import_materials_from_poscar.*
- examples/workflow/get_workflows.*
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  6. TST: test api_interoperability_showcase.ipynb in Colab

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Commits on Jun 20, 2023

  1. FIX: resolve pymatgen's import and stripout notebook's outputs

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  2. ENH: add support in the rendering script for individual notebooks pas… 

    …sed to the script as positional arguments
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  3. MNT: fix the api_interoperability_showcase.ipynb notebook and rende… 

    …r it
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  4. DOC: add API interoperability notebook to the README

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  5. [AUTO] automatically updated notebooks with the rendering script

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Commits on Jun 21, 2023

  1. MNT: rename initialize_settings.py -> notebook.py and clean it up… 

    … from unused functions
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  2. DOC: update the description of the variables in settings.py (moved … 

    …from the cleaned up `initialize_settings.py`)
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  3. MNT: run export to python scripts first before executing the .ipynb f… 

    …iles
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  4. FIX: import of get_notebook_info

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  5. [AUTO] automatically updated notebooks with the rendering script

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  6. MNT: branch update bugfix/SOF-5578-WIP -> dev

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