From 6ceb5ca5fe26d3a639b45c64358755fde713dd29 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Thu, 25 Jun 2026 18:13:42 -0700 Subject: [PATCH] chore: update GitHub org references from Exabyte-io to mat3ra - Replace all Exabyte-io/exabyte-io GitHub organization URLs with mat3ra - Rename exabyte-api-client repo reference to api-client - Rename exabyte-api-examples repo reference to api-examples - Update mkdocs-base.yml repo_name and repo_url - Update CI workflow action references - Update .gitmodules submodule URL - Update footnote link text to use Mat3ra branding - Update example JSON data organization slugs and cluster paths --- .github/workflows/build-tests.yml | 2 +- .github/workflows/s3-deploy.yml | 2 +- .gitmodules | 2 +- README.md | 4 +-- .../machine-learning-predict.json | 18 +++++------ data/example-json/machine-learning-train.json | 2 +- lang/en/docs/cli/actions/add-software.md | 4 +-- lang/en/docs/data-structured/convention.md | 2 +- .../getting-started/content-highlights.md | 12 +++---- lang/en/docs/index-guide.md | 2 +- .../infrastructure/clusters/directories.md | 6 ++-- .../docs/jupyterlite/accessing-jupyterlite.md | 2 +- .../jupyterlite/dependencies-installation.md | 2 +- .../input-output/standata-import.md | 2 +- lang/en/docs/materials/actions/set-default.md | 2 +- lang/en/docs/metadata/general.json | 2 +- .../non-scalar/workflow.md | 2 +- .../en/docs/properties/data/periodic-table.md | 2 +- lang/en/docs/rest-api/api-client.md | 4 +-- lang/en/docs/rest-api/api-examples.md | 4 +-- .../scripting/jupyter-lab/data.md | 4 +-- .../tutorials/contribute-new-application.md | 32 +++++++++---------- .../dft/electronic/valence-band-offset.md | 8 ++--- .../dft/optical/epsilon-optimal-basis.md | 2 +- lang/en/docs/tutorials/jobs-cli/qe-gpu.md | 4 +-- .../defect-point-interstitial-tin-oxide.md | 2 +- .../defect-point-pair-gallium-nitride.md | 2 +- .../defect-point-substitution-graphene.md | 2 +- .../defect-surface-island-titanium-nitride.md | 2 +- mkdocs-base.yml | 6 ++-- 30 files changed, 71 insertions(+), 71 deletions(-) diff --git a/.github/workflows/build-tests.yml b/.github/workflows/build-tests.yml index 71b94d883..c127aac44 100644 --- a/.github/workflows/build-tests.yml +++ b/.github/workflows/build-tests.yml @@ -96,7 +96,7 @@ jobs: - name: Checkout actions repository uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: - repository: Exabyte-io/actions + repository: mat3ra/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} path: actions diff --git a/.github/workflows/s3-deploy.yml b/.github/workflows/s3-deploy.yml index ccb048d53..d9ee1538b 100644 --- a/.github/workflows/s3-deploy.yml +++ b/.github/workflows/s3-deploy.yml @@ -30,7 +30,7 @@ jobs: python-version: "3.10" - name: Build pages (legacy) - uses: Exabyte-io/action-mkdocs-build@main + uses: mat3ra/action-mkdocs-build@main - name: Build split sites run: | diff --git a/.gitmodules b/.gitmodules index 4fb0abd1c..6205cf7da 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,3 @@ [submodule "esse"] path = data/esse - url = https://github.com/Exabyte-io/esse.git + url = https://github.com/mat3ra/esse.git diff --git a/README.md b/README.md index 5cf259b10..78942a776 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ For a quick installation: 2. Clone this repository: ```bash - git clone https://github.com/Exabyte-io/documentation.git + git clone https://github.com/mat3ra/documentation.git ``` 3. Setup virtual environment @@ -457,7 +457,7 @@ Including a clickable image map is done as follows. Note that absolute paths to Including resolved JSON schemas and associated examples should be done within dedicated `data.md` pages for each concept being explained. -The [markdown_include](https://github.com/Exabyte-io/markdown-include) package is used to include JSON content into markdown documents, by putting direct links to pages inside the [ESSE repository](https://github.com/Exabyte-io/exabyte-esse) instead of copying their contents in the main documentation. +The [markdown_include](https://github.com/mat3ra/markdown-include) package is used to include JSON content into markdown documents, by putting direct links to pages inside the [ESSE repository](https://github.com/mat3ra/exabyte-esse) instead of copying their contents in the main documentation. ```text === "Schema" diff --git a/data/example-json/machine-learning-predict.json b/data/example-json/machine-learning-predict.json index 9c739e1ba..bf5d9f66b 100644 --- a/data/example-json/machine-learning-predict.json +++ b/data/example-json/machine-learning-predict.json @@ -8,7 +8,7 @@ }, "owner": { "_id": "5b143a4ecd313f405b314224", - "slug": "exabyte-io", + "slug": "mat3ra", "cls": "Account" }, "schemaVersion": "0.2.0", @@ -219,7 +219,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/target.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/target.pkl" } }, { @@ -230,7 +230,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/workflow_context_file_mapping" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/workflow_context_file_mapping" } }, { @@ -241,7 +241,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/descriptors.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/descriptors.pkl" } }, { @@ -252,7 +252,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/target_scaler.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/target_scaler.pkl" } }, { @@ -263,7 +263,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/descriptor_scaler.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/descriptor_scaler.pkl" } }, { @@ -274,7 +274,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/sklearn_mlp.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/sklearn_mlp.pkl" } }, { @@ -285,7 +285,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/predictions.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/predictions.pkl" } }, { @@ -296,7 +296,7 @@ "CONTAINER": "production-20160630-cluster-001", "PROVIDER": "aws", "REGION": "us-east-1", - "NAME": "/cluster-001-share/groups/exabyte-io/exabyte-io-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/RMSE.pkl" + "NAME": "/cluster-001-share/groups/mat3ra/mat3ra-2021-ml-work/checking-ml-file-property-ec8ToqKwpWDGiyNCS/.job_context/RMSE.pkl" } } ], diff --git a/data/example-json/machine-learning-train.json b/data/example-json/machine-learning-train.json index c5bd24ba4..1555b4d0d 100644 --- a/data/example-json/machine-learning-train.json +++ b/data/example-json/machine-learning-train.json @@ -714,7 +714,7 @@ "hash": "c0c97c1dffb00371a5aec012306d9b4b", "owner": { "_id": "5b143a4ecd313f405b314224", - "slug": "exabyte-io", + "slug": "mat3ra", "cls": "Account" }, "creator": { diff --git a/lang/en/docs/cli/actions/add-software.md b/lang/en/docs/cli/actions/add-software.md index 14326927d..9ce897cdd 100644 --- a/lang/en/docs/cli/actions/add-software.md +++ b/lang/en/docs/cli/actions/add-software.md @@ -239,7 +239,7 @@ apptainer exec --nv --bind /export,/cluster-001-share pw.x - To understand the details about library paths, one may inspect modulefiles (e.g., `/cluster-001-share/compute/modulefiles/applications/espresso/7.5-cuda-12.8`) available in our clusters and [job scripts]( -https://github.com/Exabyte-io/cli-job-examples/blob/main/espresso/gpu/job.gpu.pbs) +https://github.com/mat3ra/cli-job-examples/blob/main/espresso/gpu/job.gpu.pbs) to see how it is implemented. Do not forget to use a GPU-enabled queue, such as [GOF]({{ resources_url }}/infrastructure/clusters/google/) to submit your GPU jobs. @@ -281,7 +281,7 @@ Once the job is completed, all output files will be saved under the directory from which the job was submitted. Please follow [this documentation page]( ../../jobs-cli/batch-scripts/apptainer.md) to find more about Apptainer integration. For practical templates, please visit[CLI job examples]( -https://github.com/Exabyte-io/cli-job-examples). +https://github.com/mat3ra/cli-job-examples). ## Transfer external images diff --git a/lang/en/docs/data-structured/convention.md b/lang/en/docs/data-structured/convention.md index 758adbd6d..d6e0df830 100644 --- a/lang/en/docs/data-structured/convention.md +++ b/lang/en/docs/data-structured/convention.md @@ -1,6 +1,6 @@ # ESSE Data Convention -Our approach towards storing and organizing structured data is based on the **ESSE Data Convention (EDC)** explained in the present documentation. ESSE stands for Essential Source of Schemas and Examples. The corresponding schema implementations are open-source and available in the [GitHub repository](https://github.com/Exabyte-io/esse) and as a package on [PyPI](https://pypi.org/project/mat3ra-esse/). +Our approach towards storing and organizing structured data is based on the **ESSE Data Convention (EDC)** explained in the present documentation. ESSE stands for Essential Source of Schemas and Examples. The corresponding schema implementations are open-source and available in the [GitHub repository](https://github.com/mat3ra/esse) and as a package on [PyPI](https://pypi.org/project/mat3ra-esse/). We use this convention to store and organize the information associated with the [Entities]({{ reference_url }}/entities-general/overview/) present across our platform, and their corresponding [Accounts]({{ reference_url }}/accounts/overview/) and [Permissions]({{ reference_url }}/entities-general/permissions/). The convention is designed with the aim of facilitating both the access and collaboration with regards to such entities. The fundamental practices are further elucidated in the sections below. diff --git a/lang/en/docs/getting-started/content-highlights.md b/lang/en/docs/getting-started/content-highlights.md index b3222e338..1ef1d9e86 100644 --- a/lang/en/docs/getting-started/content-highlights.md +++ b/lang/en/docs/getting-started/content-highlights.md @@ -98,15 +98,15 @@ JavaScript packages are available on [npm](https://www.npmjs.com/search?q=%40mat ### 6.2. Open-Source Repositories -- [Exabyte-io GitHub organization](https://github.com/Exabyte-io/){:target='_blank'} — data structures for materials, workflows, and properties -- [Materials Designer](https://github.com/Exabyte-io/materials-designer){:target='_blank'} — JavaScript library for web-based materials design -- [API examples](https://github.com/Exabyte-io/api-examples){:target='_blank'} — Jupyter notebooks demonstrating REST API usage +- [Mat3ra GitHub organization](https://github.com/mat3ra/){:target='_blank'} — data structures for materials, workflows, and properties +- [Materials Designer](https://github.com/mat3ra/materials-designer){:target='_blank'} — JavaScript library for web-based materials design +- [API examples](https://github.com/mat3ra/api-examples){:target='_blank'} — Jupyter notebooks demonstrating REST API usage ### 6.3. Programmatic Access (REST API) -- [Upload materials](https://github.com/Exabyte-io/api-examples/blob/main/examples/material/create_material.ipynb){:target='_blank'} -- [Run simulations and extract properties as JSON](https://github.com/Exabyte-io/api-examples/blob/main/examples/job/run-simulations-and-extract-properties.ipynb){:target='_blank'} -- [All API examples (GitHub)](https://github.com/Exabyte-io/api-examples){:target='_blank'} +- [Upload materials](https://github.com/mat3ra/api-examples/blob/main/examples/material/create_material.ipynb){:target='_blank'} +- [Run simulations and extract properties as JSON](https://github.com/mat3ra/api-examples/blob/main/examples/job/run-simulations-and-extract-properties.ipynb){:target='_blank'} +- [All API examples (GitHub)](https://github.com/mat3ra/api-examples){:target='_blank'} ## 7. Learning Resources diff --git a/lang/en/docs/index-guide.md b/lang/en/docs/index-guide.md index 924fc4054..030ac006b 100644 --- a/lang/en/docs/index-guide.md +++ b/lang/en/docs/index-guide.md @@ -165,7 +165,7 @@ Platform access, notebook environments, and software management. diff --git a/lang/en/docs/infrastructure/clusters/directories.md b/lang/en/docs/infrastructure/clusters/directories.md index d5f9c1740..3362bb677 100644 --- a/lang/en/docs/infrastructure/clusters/directories.md +++ b/lang/en/docs/infrastructure/clusters/directories.md @@ -6,7 +6,7 @@ The following directories are present under the home folder of each cluster (ref . ├── data ├── dropbox => /dropbox/gmogni -├── exabyte-io => /cluster-001-share/groups/exabyte-io +├── mat3ra => /cluster-001-share/groups/mat3ra └── job_script_templates => /export/compute/job_script_templates ``` @@ -33,9 +33,9 @@ The "dropbox" and "job_script_templates" folders are present under both Cluster ## Shared Folders for Organizations -Simulations data for [Organizations]({{ reference_url }}/collaboration/organizations/overview/) (collaborative [accounts]({{ reference_url }}/accounts/overview/)) is stored in a dedicated **shared folder** accessible by its **members only**. This shared folder bears the same name as the Organization itself: for example, "exabyte-io" in the visual above. Simulation files present under this data are organized according to the Project/Job based directory naming explained below. +Simulations data for [Organizations]({{ reference_url }}/collaboration/organizations/overview/) (collaborative [accounts]({{ reference_url }}/accounts/overview/)) is stored in a dedicated **shared folder** accessible by its **members only**. This shared folder bears the same name as the Organization itself: for example, "mat3ra" in the visual above. Simulation files present under this data are organized according to the Project/Job based directory naming explained below. -Each organization of which the user is member has its own corresponding shared directory. For example, organization `exabyte-io` has its folder under the path `/share/groups/exabyte-io/`. +Each organization of which the user is member has its own corresponding shared directory. For example, organization `mat3ra` has its folder under the path `/share/groups/mat3ra/`. ## Temporary Data diff --git a/lang/en/docs/jupyterlite/accessing-jupyterlite.md b/lang/en/docs/jupyterlite/accessing-jupyterlite.md index 631cb511c..4e05541ad 100644 --- a/lang/en/docs/jupyterlite/accessing-jupyterlite.md +++ b/lang/en/docs/jupyterlite/accessing-jupyterlite.md @@ -21,7 +21,7 @@ To access JupyterLite directly, navigate to the following URL: https://jupyterlite.mat3ra.com/lab/index.html ``` -To access the Introduction notebook summarizing the functionality available in [mat3ra-made](https://github.com/Exabyte-io/made): +To access the Introduction notebook summarizing the functionality available in [mat3ra-made](https://github.com/mat3ra/made): ``` https://jupyterlite.mat3ra.com/lab/tree?path=made/Introduction.ipynb diff --git a/lang/en/docs/jupyterlite/dependencies-installation.md b/lang/en/docs/jupyterlite/dependencies-installation.md index 32c35ce7f..e2521526c 100644 --- a/lang/en/docs/jupyterlite/dependencies-installation.md +++ b/lang/en/docs/jupyterlite/dependencies-installation.md @@ -21,7 +21,7 @@ from utils.jupyterlite import get_materials ## Listing notebook dependencies in `config.yaml` Some of the necessary packages are compiled into pure Python wheels and provided inside the `mat3ra-api-examples` package. In top-level `packages` folder. -The dependencies for each notebook and default ones are listed in the [`config.yml` file]("https://github.com/Exabyte-io/api-examples/blob/5e0109589da981b60fec1c1cfcae1977abbbd8ec/config.yml") on the top-level. +The dependencies for each notebook and default ones are listed in the [`config.yml` file]("https://github.com/mat3ra/api-examples/blob/5e0109589da981b60fec1c1cfcae1977abbbd8ec/config.yml") on the top-level. To install packages required for the notebook, one can use `install_packages` function from `utils.jupyterlite` module and provide the name of the notebook and the relative path to the `config.yml` file: diff --git a/lang/en/docs/materials-designer/header-menu/input-output/standata-import.md b/lang/en/docs/materials-designer/header-menu/input-output/standata-import.md index b3220f5b4..21468e475 100644 --- a/lang/en/docs/materials-designer/header-menu/input-output/standata-import.md +++ b/lang/en/docs/materials-designer/header-menu/input-output/standata-import.md @@ -23,4 +23,4 @@ Materials (Graphene and Ni in this case) should now be available in the material ## Links -1. Standata repository on GitHub. +1. Standata repository on GitHub. diff --git a/lang/en/docs/materials/actions/set-default.md b/lang/en/docs/materials/actions/set-default.md index d3d9c0e2d..8639dfc41 100644 --- a/lang/en/docs/materials/actions/set-default.md +++ b/lang/en/docs/materials/actions/set-default.md @@ -4,4 +4,4 @@ The initial default material for a new Exabyte account is set to FCC Silicon [^1 ## Links -[^1]: [Example Si FCC material, Exabyte Platform Website](https://platform.mat3ra.com/exabyte-io/materials/cMK8Z5hZMo23iDb9Z) +[^1]: [Example Si FCC material, Exabyte Platform Website](https://platform.mat3ra.com/mat3ra/materials/cMK8Z5hZMo23iDb9Z) diff --git a/lang/en/docs/metadata/general.json b/lang/en/docs/metadata/general.json index 118243d5f..5eaa783a1 100644 --- a/lang/en/docs/metadata/general.json +++ b/lang/en/docs/metadata/general.json @@ -3,7 +3,7 @@ "chemistry", "cloud computing", "exabyte", - "exabyte-io", + "mat3ra", "high-performance computing", "HPC", "industry", diff --git a/lang/en/docs/properties-directory/non-scalar/workflow.md b/lang/en/docs/properties-directory/non-scalar/workflow.md index 309746615..654b5db90 100644 --- a/lang/en/docs/properties-directory/non-scalar/workflow.md +++ b/lang/en/docs/properties-directory/non-scalar/workflow.md @@ -8,7 +8,7 @@ workflow being generated and placed in the user's account. ## Creation during ML Jobs If any unit in the workflow has the `workflow:pyml_predict` property, -[Express will be called](https://github.com/Exabyte-io/express/blob/dev/express/properties/workflow.py) to construct +[Express will be called](https://github.com/mat3ra/express/blob/dev/express/properties/workflow.py) to construct the new predict workflow. The following process is performed to convert a workflow from "Train" to "Predict" mode: - The `IS_WORKFLOW_RUNNING_TO_PREDICT` flag is set to `True` diff --git a/lang/en/docs/properties/data/periodic-table.md b/lang/en/docs/properties/data/periodic-table.md index 31b3b3156..14f3fa562 100644 --- a/lang/en/docs/properties/data/periodic-table.md +++ b/lang/en/docs/properties/data/periodic-table.md @@ -6,4 +6,4 @@ We assembled the data using the open-source Ref. [^1] below. ## Links -[^1]: [Exabyte.io Periodic Table Data, JSON, Github Repository](https://github.com/Exabyte-io/periodic-table) +[^1]: [Exabyte.io Periodic Table Data, JSON, Github Repository](https://github.com/mat3ra/periodic-table) diff --git a/lang/en/docs/rest-api/api-client.md b/lang/en/docs/rest-api/api-client.md index aaaab195a..ff8f6c955 100644 --- a/lang/en/docs/rest-api/api-client.md +++ b/lang/en/docs/rest-api/api-client.md @@ -2,7 +2,7 @@ ## Python -We have deployed a python-based [**API client**](https://github.com/Exabyte-io/exabyte-api-client)[^1] providing access to the RESTful-API endpoints. Readers are referred to the source code repository linked below for more information. +We have deployed a python-based [**API client**](https://github.com/mat3ra/api-client)[^1] providing access to the RESTful-API endpoints. Readers are referred to the source code repository linked below for more information. ## Other @@ -10,6 +10,6 @@ Please [contact us]({{ interface_url }}/ui/support/) if you are interested in an ## Links -[^1]: [Exabyte API Client repository, Github](https://github.com/Exabyte-io/exabyte-api-client) +[^1]: [Mat3ra API Client repository, Github](https://github.com/mat3ra/api-client) ///FOOTNOTES GO HERE/// diff --git a/lang/en/docs/rest-api/api-examples.md b/lang/en/docs/rest-api/api-examples.md index 2dd2a31d3..1ec1e9a40 100644 --- a/lang/en/docs/rest-api/api-examples.md +++ b/lang/en/docs/rest-api/api-examples.md @@ -2,10 +2,10 @@ We published an open-source repository[^1] with examples for performing some of the most common tasks in the Mat3ra.com platform through the API in Jupyter Notebook format. Readers are referred to the original online link below for more information. -Rendered notebooks are available in the [API Examples repository](https://github.com/Exabyte-io/exabyte-api-examples). +Rendered notebooks are available in the [API Examples repository](https://github.com/mat3ra/api-examples). ## Links -[^1]: [Exabyte API Examples repository, GitHub](https://github.com/Exabyte-io/exabyte-api-examples) +[^1]: [Mat3ra API Examples repository, GitHub](https://github.com/mat3ra/api-examples) ///FOOTNOTES GO HERE/// diff --git a/lang/en/docs/software-directory/scripting/jupyter-lab/data.md b/lang/en/docs/software-directory/scripting/jupyter-lab/data.md index a6054a7b8..946d7b38e 100644 --- a/lang/en/docs/software-directory/scripting/jupyter-lab/data.md +++ b/lang/en/docs/software-directory/scripting/jupyter-lab/data.md @@ -18,8 +18,8 @@ We present in what follows the [structured representation]({{ data_url }}/data-s 1. Initially, the root of the Dropbox folder is passed to the application on the start, so the files at the root of the [Dropbox]({{ resources_url }}/data-in-objectstorage/dropbox/) directory can be accessed 2. Upon each "Save and Checkpoint" action invoked inside the notebook, the ipynb file is overwritten. A new version is stored in the file system, and a checkpoint is saved to the job inside its directory both in the [command-line]({{ cli_url }}/jobs-cli/batch-scripts/directories/#working-directory) and on the [web interface]({{ resources_url }}/data-in-objectstorage/files/). -3. All notebooks have access to the filesystem accessible to the user on the corresponding computational node, namely the [home]({{ resources_url }}/infrastructure/clusters/directories/) and [share]({{ resources_url }}/infrastructure/clusters/directories/) directories. For example, the following command will list the shared directory for the account "exabyte-io", when invoked inside the Jupyter Notebook running on "cluster-007": +3. All notebooks have access to the filesystem accessible to the user on the corresponding computational node, namely the [home]({{ resources_url }}/infrastructure/clusters/directories/) and [share]({{ resources_url }}/infrastructure/clusters/directories/) directories. For example, the following command will list the shared directory for the account "mat3ra", when invoked inside the Jupyter Notebook running on "cluster-007": ```bash - ls -lhta /cluster-007-share/groups/exabyte-io + ls -lhta /cluster-007-share/groups/mat3ra ``` diff --git a/lang/en/docs/tutorials/contribute-new-application.md b/lang/en/docs/tutorials/contribute-new-application.md index 267a4ef0b..f05edb39e 100644 --- a/lang/en/docs/tutorials/contribute-new-application.md +++ b/lang/en/docs/tutorials/contribute-new-application.md @@ -5,14 +5,14 @@ 1. **Build the Image:** Package your application into an Apptainer container. Create a PR to the [application-containers-public]( - https://github.com/Exabyte-io/application-containers-public) repository + https://github.com/mat3ra/application-containers-public) repository with the Apptainer `.def` file and register it in `manifest.yml`. Merge this PR first so the container image is built and published to the GitHub Container Registry (GHCR). 2. **Update the Metadata:** Add the application's YAML metadata, templates, and executables, ensuring your image tag matches Step 1 exactly. Create a PR - to the [standata](https://github.com/Exabyte-io/standata) repository. Once + to the [standata](https://github.com/mat3ra/standata) repository. Once merged and deployed, the application will be available on both the web-interface and the CLI. @@ -40,12 +40,12 @@ Contributing a new application involves creating Pull Requests (PRs) to two repositories: [**application-containers-public**]( -https://github.com/Exabyte-io/application-containers-public) holds the Apptainer +https://github.com/mat3ra/application-containers-public) holds the Apptainer definition files and a `manifest.yml` that drives a GitHub Actions (GHA) workflow. On merge, GHA builds each image and pushes it to the GitHub Container Registry (GHCR). -[**standata**](https://github.com/Exabyte-io/standata) holds the platform +[**standata**](https://github.com/mat3ra/standata) holds the platform metadata, including application name, version, build flavor, the GHCR image tag to pull, and the runtime environment variables. The platform reads this repository to populate the application dropdown in the web-interface. Necessary @@ -84,8 +84,8 @@ flowchart TB ### 2.1. Fork and clone the repository -First, fork [github.com/Exabyte-io/application-containers-public]( -https://github.com/Exabyte-io/application-containers-public) on GitHub, then +First, fork [github.com/mat3ra/application-containers-public]( +https://github.com/mat3ra/application-containers-public) on GitHub, then clone the fork locally. The top-level layout is: ``` @@ -113,7 +113,7 @@ possible: ```singularity Bootstrap: oras -From: ghcr.io/exabyte-io/application-containers-public/almalinux-apptainer-gnu:9.7-2 +From: ghcr.io/mat3ra/application-containers-public/almalinux-apptainer-gnu:9.7-2 ``` This reuses tested toolchains and keeps build times short. @@ -174,14 +174,14 @@ checks whether each tag already exists in GHCR, and if not, runs After merge, the image is available at: ```bash -apptainer pull oras://ghcr.io/exabyte-io/application-containers-public/espresso:7.5-gnu-1 +apptainer pull oras://ghcr.io/mat3ra/application-containers-public/espresso:7.5-gnu-1 ``` The image name, and tag are needed in the next section. ### 2.5. Example Pull Requests -- [GNU build of Quantum ESPRESSO 7.5](https://github.com/Exabyte-io/application-containers-public/pull/7/changes) -- [Intel build of LAMMPS](https://github.com/Exabyte-io/application-containers-public/pull/9/changes) +- [GNU build of Quantum ESPRESSO 7.5](https://github.com/mat3ra/application-containers-public/pull/7/changes) +- [Intel build of LAMMPS](https://github.com/mat3ra/application-containers-public/pull/9/changes) ## 3. `standata` repository @@ -195,7 +195,7 @@ The image name, and tag are needed in the next section. ### 3.1. Fork and clone the repository -Fork [github.com/Exabyte-io/standata](https://github.com/Exabyte-io/standata) +Fork [github.com/mat3ra/standata](https://github.com/mat3ra/standata) and clone locally. The relevant subtree is: ``` @@ -372,8 +372,8 @@ has been merged and the image is live in GHCR. Commit the generated files under `data/` and `dist/` produced by the build step above. ### 3.8. Example Pull Requests -- [Quantum ESPRESSO 7.5](https://github.com/Exabyte-io/standata/pull/109/changes) -- [LAMMPS](https://github.com/Exabyte-io/standata/pull/91/changes) +- [Quantum ESPRESSO 7.5](https://github.com/mat3ra/standata/pull/109/changes) +- [LAMMPS](https://github.com/mat3ra/standata/pull/91/changes) One may ignore the auto-generated files under `data/`, `dist/`, and `src/` directories while reviewing the PR changes. @@ -413,6 +413,6 @@ application is also available via modulefile for CLI use. ## 5. References - Apptainer Definition and container building: [Adding New Software](/cli/actions/add-software) -- Container repository: [github.com/Exabyte-io/application-containers-public](https://github.com/Exabyte-io/application-containers-public) -- Metadata repository: [github.com/Exabyte-io/standata](https://github.com/Exabyte-io/standata) -- Published images: [Exabyte-io packages on GHCR](https://github.com/orgs/Exabyte-io/packages?repo_name=application-containers-public) +- Container repository: [github.com/mat3ra/application-containers-public](https://github.com/mat3ra/application-containers-public) +- Metadata repository: [github.com/mat3ra/standata](https://github.com/mat3ra/standata) +- Published images: [Mat3ra packages on GHCR](https://github.com/orgs/mat3ra/packages?repo_name=application-containers-public) diff --git a/lang/en/docs/tutorials/dft/electronic/valence-band-offset.md b/lang/en/docs/tutorials/dft/electronic/valence-band-offset.md index d544747d5..423daebc3 100644 --- a/lang/en/docs/tutorials/dft/electronic/valence-band-offset.md +++ b/lang/en/docs/tutorials/dft/electronic/valence-band-offset.md @@ -42,9 +42,9 @@ Three materials are required, corresponding to the MoS2/WS22 monolayer](https://platform.mat3ra.com/exabyte-io/materials/5JcsfbBPKFWjxGXkX) -- [MoS2 monolayer](https://platform.mat3ra.com/exabyte-io/materials/Cyr7Y6sefZsmZo6bH) +- [MoS2/WS2 heterostructure](https://platform.mat3ra.com/mat3ra/materials/cxgeoQwPJQJbgA2aD) +- [WS2 monolayer](https://platform.mat3ra.com/mat3ra/materials/5JcsfbBPKFWjxGXkX) +- [MoS2 monolayer](https://platform.mat3ra.com/mat3ra/materials/Cyr7Y6sefZsmZo6bH) !!!warning "Material order" The VBO workflow assumes the interface structure corresponds to the first material. The interface structure must be loaded first. @@ -54,7 +54,7 @@ The initial interface structure was taken from [materialsproject.org](https://ma The [workflow]({{ reference_url }}/workflows/overview/) for calculating the VBO can be [imported]({{ interface_url }}/workflows/actions/copy-bank/) from the [Workflows Bank]({{ reference_url }}/workflows/bank/) into the account-owned [collection]({{ reference_url }}/accounts/collections/). The workflow can then be [selected]({{ interface_url }}/jobs-designer/actions-header-menu/select-workflow/) and added to the [job being created]({{ interface_url }}/jobs-designer/workflow-tab/). -A [representation of this workflow](https://github.com/Exabyte-io/wode.js/blob/2022.11.16-0/assets/workflows/espresso/valence_band_offset.yml) is also available in the Mat3ra workflow definitions repository ([wode.js](https://github.com/Exabyte-io/wode.js)). +A [representation of this workflow](https://github.com/mat3ra/wode.js/blob/2022.11.16-0/assets/workflows/espresso/valence_band_offset.yml) is also available in the Mat3ra workflow definitions repository ([wode.js](https://github.com/mat3ra/wode.js)). [![Valence Band Offset Workflow](../../../images/tutorials/valence-band-offset-workflow.png "Valence Band Offset Workflow")](../../../images/tutorials/valence-band-offset-workflow.png) diff --git a/lang/en/docs/tutorials/dft/optical/epsilon-optimal-basis.md b/lang/en/docs/tutorials/dft/optical/epsilon-optimal-basis.md index 56906ff1f..f69de131d 100644 --- a/lang/en/docs/tutorials/dft/optical/epsilon-optimal-basis.md +++ b/lang/en/docs/tutorials/dft/optical/epsilon-optimal-basis.md @@ -2,7 +2,7 @@ This tutorial demonstrates how to calculate the dielectric function of silicon using the SIMPLE.x program in Quantum ESPRESSO, which employs optimal basis functions for optical property calculations. The detailed physics behind this method is described in: [SIMPLE code: Optical properties with optimal basis functions, Prandini, G., Galante, M., Marzari, N., & Umari, P., Computer Physics Communications, **240**, 106 (2019)](https://doi.org/10.1016/j.cpc.2019.02.016). -The workflow below replicates [example 5 from the Quantum ESPRESSO GWW directory](https://gitlab.com/QEF/q-e/-/tree/qe-7.3/GWW/examples/). Input and reference output files are also available in the [CLI-job-examples repository](https://github.com/Exabyte-io/cli-job-examples/tree/main/espresso/simple.x). +The workflow below replicates [example 5 from the Quantum ESPRESSO GWW directory](https://gitlab.com/QEF/q-e/-/tree/qe-7.3/GWW/examples/). Input and reference output files are also available in the [CLI-job-examples repository](https://github.com/mat3ra/cli-job-examples/tree/main/espresso/simple.x). ## 1. Create the workflow diff --git a/lang/en/docs/tutorials/jobs-cli/qe-gpu.md b/lang/en/docs/tutorials/jobs-cli/qe-gpu.md index 0fb8238d8..0de2a910c 100644 --- a/lang/en/docs/tutorials/jobs-cli/qe-gpu.md +++ b/lang/en/docs/tutorials/jobs-cli/qe-gpu.md @@ -19,10 +19,10 @@ Connect to the login node via [SSH client]({{ cli_url }}/remote-connection/ssh/) ## 2. Clone the example repository -The example job is available in the git repository [exabyte-io/cli-job-examples](https://github.com/exabyte-io/cli-job-examples). Clone the repository to the working directory: +The example job is available in the git repository [mat3ra/cli-job-examples](https://github.com/mat3ra/cli-job-examples). Clone the repository to the working directory: ```bash -git clone https://github.com/exabyte-io/cli-job-examples +git clone https://github.com/mat3ra/cli-job-examples cd cli-job-examples git lfs pull cd espresso/gpu diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index d88512350..d44f3c579 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -28,7 +28,7 @@ This tutorial demonstrates how to create an oxygen interstitial defect in tin mo Physical Review B 74, 195128 (2006) [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] -We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [Voronoi](https://github.com/Exabyte-io/made/blob/9e13b350eaaa5d49c81a3b30f76c165480825d72/src/py/mat3ra/made/tools/build/defect/builders.py#L125) placement method. +We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [Voronoi](https://github.com/mat3ra/made/blob/9e13b350eaaa5d49c81a3b30f76c165480825d72/src/py/mat3ra/made/tools/build/defect/builders.py#L125) placement method. ![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md index 47f24f4a4..c1e0215c5 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -78,7 +78,7 @@ Find `create_point_defect_pair.ipynb` in the list of notebooks and click/double- ### 4.3. Open and modify the notebook -Next, edit `create_point_defect_pair.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L257) containing the approximate coordinates of the atoms to replace. +Next, edit `create_point_defect_pair.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/mat3ra/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L257) containing the approximate coordinates of the atoms to replace. Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index d97d7165d..94398eb36 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -69,7 +69,7 @@ Find `create_point_defect.ipynb` in the list of notebooks and click/double-click ### 4.3. Open and modify the notebook -Next, edit `create_point_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L32) containing the approximate coordinates of the atoms to replace. +Next, edit `create_point_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/mat3ra/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L32) containing the approximate coordinates of the atoms to replace. Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 7f2b394c6..41a229d9e 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -119,7 +119,7 @@ Find `create_island_defect.ipynb` in the list of notebooks and double-click open ### 4.2. Modify the notebook -Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. +Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/mat3ra/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. With the same TiN material selected in the materials input and coordinates for the island vertices from the previous step, the user can create the island on the surface. diff --git a/mkdocs-base.yml b/mkdocs-base.yml index 0a937f9fd..aa112493a 100644 --- a/mkdocs-base.yml +++ b/mkdocs-base.yml @@ -1,5 +1,5 @@ -repo_name: 'exabyte-io/documentation' -repo_url: 'https://github.com/exabyte-io/documentation' +repo_name: 'mat3ra/documentation' +repo_url: 'https://github.com/mat3ra/documentation' edit_uri: 'edit/main/lang/en/docs/' extra_css: @@ -31,7 +31,7 @@ extra: - /extra/js/preload.js social: - icon: fontawesome/brands/github - link: https://github.com/exabyte-io + link: https://github.com/mat3ra - icon: fontawesome/brands/youtube link: https://www.youtube.com/c/Mat3ra/videos - icon: fontawesome/brands/linkedin