Post rename updates (#816)

* post merge name changes

* some more updates

* updates

Author: ktangsali

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -14,23 +14,23 @@
 # limitations under the License.
 
 name: Bug Report
-description: File a bug report for Modulus (Core)
+description: File a bug report for PhysicsNeMo (Core)
 title: "🐛[BUG]: "
 labels: ["bug", "? - Needs Triage"]
 
 body:
   - type: markdown
     attributes:
       value: |
-        Thanks for taking the time to help Modulus and fill out this bug report!
-        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/modulus/blob/main/CONTRIBUTING.md)
-        - You also confirm that you have searched the [open bugs](https://github.com/NVIDIA/modulus/issues) and have found no duplicates for this request
+        Thanks for taking the time to help PhysicsNeMo and fill out this bug report!
+        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/physicsnemo/blob/main/CONTRIBUTING.md)
+        - You also confirm that you have searched the [open bugs](https://github.com/NVIDIA/physicsnemo/issues) and have found no duplicates for this request
 
   - type: input
     id: version
     attributes:
       label: Version
-      description: What version of Modulus are you running?
+      description: What version of PhysicsNeMo are you running?
       placeholder: "example: 0.9.0"
     validations:
       required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
   - name: Ask a Question
-    url: https://forums.developer.nvidia.com/c/physics-simulation/modulus-physics-ml-model-framework
+    url: https://forums.developer.nvidia.com/t/welcome-to-the-physicsnemo-ml-model-framework-forum/178556
     about: Thanks for taking the time to ask us a question!

.github/ISSUE_TEMPLATE/documentation_request.yml

@@ -14,17 +14,17 @@
 # limitations under the License.
 
 name: Documentation Request
-description: Request updates or additions to Modulus (Core) documentation
+description: Request updates or additions to PhysicsNeMo (Core) documentation
 title: "📚[DOC]: "
 labels: ["documentation", "? - Needs Triage"]
 
 body:
   - type: markdown
     attributes:
       value: |
-        Thanks for taking the time to help Modulus and improve our documentation!
-        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/modulus/blob/main/CONTRIBUTING.md)
-        - You also confirm that you have searched the [open documentation issues](https://github.com/NVIDIA/modulus/issues) and have found no duplicates for this request
+        Thanks for taking the time to help PhysicsNeMo and improve our documentation!
+        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/physicsnemo/blob/main/CONTRIBUTING.md)
+        - You also confirm that you have searched the [open documentation issues](https://github.com/NVIDIA/physicsnemo/issues) and have found no duplicates for this request
 
   - type: dropdown
     id: criticality

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -14,17 +14,17 @@
 # limitations under the License.
 
 name: Feature Request
-description: Request new or improved functionality or changes to existing Modulus (Core) functionality
+description: Request new or improved functionality or changes to existing PhysicsNeMo (Core) functionality
 title: "🚀[FEA]: "
 labels: ["enhancement", "? - Needs Triage"]
 
 body:
   - type: markdown
     attributes:
       value: |
-        Thanks for taking the time to help Modulus and fill out this feature request!
-        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/modulus/blob/main/CONTRIBUTING.md)
-        - You also confirm that you have searched the [open documentation issues](https://github.com/NVIDIA/modulus/issues) and have found no duplicates for this request
+        Thanks for taking the time to help PhysicsNeMo and fill out this feature request!
+        - By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/NVIDIA/physicsnemo/blob/main/CONTRIBUTING.md)
+        - You also confirm that you have searched the [open documentation issues](https://github.com/NVIDIA/physicsnemo/issues) and have found no duplicates for this request
 
   - type: dropdown
     id: new_or_improvement

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,5 @@
 <!-- markdownlint-disable MD013-->
-# Modulus Pull Request
+# PhysicsNeMo Pull Request
 
 ## Description
 <!-- Provide a standalone description of changes in this PR. -->
@@ -8,11 +8,11 @@
 
 ## Checklist
 
-- [ ] I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/modulus/blob/main/CONTRIBUTING.md).
+- [ ] I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/physicsnemo/blob/main/CONTRIBUTING.md).
 - [ ] New or existing tests cover these changes.
 - [ ] The documentation is up to date with these changes.
-- [ ] The [CHANGELOG.md](https://github.com/NVIDIA/modulus/blob/main/CHANGELOG.md) is up to date with these changes.
-- [ ] An [issue](https://github.com/NVIDIA/modulus/issues) is linked to this pull request.
+- [ ] The [CHANGELOG.md](https://github.com/NVIDIA/physicsnemo/blob/main/CHANGELOG.md) is up to date with these changes.
+- [ ] An [issue](https://github.com/NVIDIA/physicsnemo/issues) is linked to this pull request.
 
 ## Dependencies
 

.gitlab/issue_templates/bug.md

@@ -1,6 +1,6 @@
 # Bug
 
-For technical questions please refer to our [forum](https://forums.developer.nvidia.com/c/physics-simulation/modulus-physics-ml-model-framework/443).
+For technical questions please refer to our [forum](https://forums.developer.nvidia.com/t/welcome-to-the-physicsnemo-ml-model-framework-forum/178556).
 
 Before submitting an issue, please review the existing issues to avoid duplicates.
 
@@ -35,12 +35,12 @@ python collect_env.py
 - GPU models and configuration:
 - Versions of any other relevant libraries:
 
-## Modulus Info
+## PhysicsNeMo Info
 
 Please fill out the list below:
 
-- Modulus version:
-- How Modulus is used (Docker image/ bare-metal installation):
+- PhysicsNeMo version:
+- How PhysicsNeMo is used (Docker image/ bare-metal installation):
 - (If using OptiX) OptiX version:
 - Exact command to reproduce:
-- (If using Modulus Docker image): Exact docker-run command:
+- (If using PhysicsNeMo Docker image): Exact docker-run command:

.gitlab/issue_templates/documentation.md

@@ -1,14 +1,14 @@
 # Documentation
 
-For technical questions please refer to our [forum](https://forums.developer.nvidia.com/c/physics-simulation/modulus-physics-ml-model-framework/443).
+For technical questions please refer to our [forum](https://forums.developer.nvidia.com/t/welcome-to-the-physicsnemo-ml-model-framework-forum/178556).
 
 Before submitting an issue, please review the existing issues to avoid duplicates.
 
 For documenation issues, please preface the title with [documentation].
 
 ## The documentation issue
 
-A clear and concise description of what content in Modulus documentation is an issue.
+A clear and concise description of what content in PhysicsNeMo documentation is an issue.
 
 ## Suggest a potential alternative/fix
 

.gitlab/issue_templates/feature_request.md

@@ -1,6 +1,6 @@
 # Feature Request
 
-For technical questions please refer to our [forum](https://forums.developer.nvidia.com/c/physics-simulation/modulus-physics-ml-model-framework/443).
+For technical questions please refer to our [forum](https://forums.developer.nvidia.com/t/welcome-to-the-physicsnemo-ml-model-framework-forum/178556).
 
 Before submitting an issue, please review the existing issues to avoid duplicates.
 

.gitlab/issue_templates/security.md

@@ -1,13 +1,13 @@
 # Security
 
-For technical questions please refer to our [forum](https://forums.developer.nvidia.com/c/physics-simulation/modulus-physics-ml-model-framework/443).
+For technical questions please refer to our [forum](https://forums.developer.nvidia.com/t/welcome-to-the-physicsnemo-ml-model-framework-forum/178556).
 
 Before submitting an issue, please review the existing issues to avoid duplicates.
 
 For security issues, please preface the title with [security].
 
 ## The Security Issue
 
-If you believe you have found a security vulnerability in Modulus, we encourage you to
+If you believe you have found a security vulnerability in PhysicsNeMo, we encourage you to
 let us know right away.
 We will investigate all legitimate reports and do our best to quickly fix the problem.

.gitlab/merge_request_templates/Default.md

@@ -1,4 +1,4 @@
-# Modulus Pull Request
+# PhysicsNeMo Pull Request
 
 ## Description
 <!-- Provide a standalone description of changes in this PR. -->
@@ -7,10 +7,10 @@
 
 ## Checklist
 
-- [ ] I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/modulus/blob/main/CONTRIBUTING.md).
+- [ ] I am familiar with the [Contributing Guidelines](https://github.com/NVIDIA/physicsnemo/blob/main/CONTRIBUTING.md).
 - [ ] New or existing tests cover these changes.
 - [ ] The documentation is up to date with these changes.
-- [ ] The [CHANGELOG.md](https://github.com/NVIDIA/modulus/blob/main/CHANGELOG.md) is
+- [ ] The [CHANGELOG.md](https://github.com/NVIDIA/physicsnemo/blob/main/CHANGELOG.md) is
 up to date with these changes.
 
 ## Dependencies

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     rev: 22.10.0
     hooks:
     - id: black
-      exclude: "(docs|modulus/experimental)"
+      exclude: "(docs|physicsnemo/experimental)"
 
 -   repo: https://github.com/econchick/interrogate
     rev: 1.7.0
@@ -31,7 +31,7 @@ repos:
           "--ignore-magic", "--fail-under=99", "--exclude=['setup.py', 'test', 'build', 'docs']",  
           "--ignore-regex=['forward', 'backward', 'reset_parameters', 'extra_repr', 'MetaData', 'apply_activation','exec_activation']", 
           "--color", "--"]
-      exclude: ^modulus/internal/|^modulus/experimental/|^docs/
+      exclude: ^physicsnemo/internal/|^physicsnemo/experimental/|^docs/
 
 -   repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.35.0

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
-title: "NVIDIA Modulus: An open-source framework for physics-based deep learning in science and engineering"
+title: "NVIDIA PhysicsNeMo: An open-source framework for physics-based deep learning in science and engineering"
 date-released: "2023-02-24"
 authors:
-  - name: "Modulus Contributors"
-repository-code: "https://github.com/NVIDIA/modulus"
+  - name: "PhysicsNeMo Contributors"
+repository-code: "https://github.com/NVIDIA/physicsnemo"

CONTRIBUTING.md

@@ -18,7 +18,7 @@ contributing to the project. One way to do this is to create an issue discussing
 your thoughts. It might be that a very similar feature is under development or
 already exists, so an issue is a great starting point. If you are looking for an
 issue to resolve that will help, refer to the
-[issue](https://github.com/NVIDIA/modulus/issues) section.
+[issue](https://github.com/NVIDIA/physicsnemo/issues) section.
 If you are considering collaborating with NVIDIA PhysicsNeMo team to enhance PhysicsNeMo,
 fill this [proposal form](https://forms.gle/fYsbZEtgRWJUQ3oQ9) and
 we will get back to you.
@@ -30,7 +30,7 @@ we will get back to you.
 Developer workflow for code contributions is as follows:
 
 1. Developers must first [fork](https://help.github.com/en/articles/fork-a-repo)
-the [upstream](https://github.com/NVIDIA/Modulus) PhysicsNeMo repository.
+the [upstream](https://github.com/NVIDIA/physicsnemo) PhysicsNeMo repository.
 
 2. Git clone the forked repository and push changes to the personal fork.
 
@@ -215,8 +215,8 @@ The pipeline has following stages:
     To run pytest locally you can simply run `pytest` inside the `test` folder.
 
     While writing these tests, we encourage you to make use of the
-    [`@nfs_data_or_fail`](https://github.com/NVIDIA/modulus/blob/main/test/pytest_utils.py#L92)
-    and the [`@import_of_fail`](https://github.com/NVIDIA/modulus/blob/main/test/pytest_utils.py#L25)
+    [`@nfs_data_or_fail`](https://github.com/NVIDIA/physicsnemo/blob/main/test/pytest_utils.py#L92)
+    and the [`@import_of_fail`](https://github.com/NVIDIA/physicsnemo/blob/main/test/pytest_utils.py#L25)
     decorators to appropriately skip your tests for developers and users not having your
     test specific datasets and dependencies respectively. The CI has these datasets and
     dependencies so your tests will get executed during CI.

Dockerfile

@@ -94,7 +94,7 @@ ENV DGLBACKEND=$DGL_BACKEND
 ARG DGL_ARM64_WHEEL
 ENV DGL_ARM64_WHEEL=${DGL_ARM64_WHEEL:-unknown}
 
-# TODO: this is a workaround as dgl is not yet shipping arm compatible wheels for CUDA 12.x: https://github.com/NVIDIA/modulus/issues/432
+# TODO: this is a workaround as dgl is not yet shipping arm compatible wheels for CUDA 12.x: https://github.com/NVIDIA/physicsnemo/issues/432
 RUN if [ "$TARGETPLATFORM" = "linux/arm64" ] && [ "$DGL_ARM64_WHEEL" != "unknown" ]; then \
         echo "Custom DGL wheel $DGL_ARM64_WHEEL for $TARGETPLATFORM exists, installing!" && \
         pip install --no-cache-dir --no-deps /physicsnemo/deps/${DGL_ARM64_WHEEL}; \
@@ -135,7 +135,7 @@ ARG TARGETPLATFORM
 # TODO: Remove hacky downgrade of netCDF4 package. netCDF4 v1.7.1 has following 
 # issue: https://github.com/Unidata/netcdf4-python/issues/1343
 # This workaround is only added for the CI systems which run pytest only once. 
-# For more details, refer: https://github.com/NVIDIA/modulus/issues/608
+# For more details, refer: https://github.com/NVIDIA/physicsnemo/issues/608
 RUN pip install --no-cache-dir "netcdf4>=1.6.3,<1.7.1"
 
 RUN pip install --no-cache-dir "mlflow>=2.1.1"

FAQ.md

@@ -11,7 +11,7 @@
 ## What is the recommended hardware for training using PhysicsNeMo framework?
 
 Please refer to the recommended hardware section:
-[System Requirments](https://docs.nvidia.com/deeplearning/modulus/getting-started/index.html#system-requirements)
+[System Requirments](https://docs.nvidia.com/deeplearning/physicsnemo/getting-started/index.html#system-requirements)
 
 ## What model architectures are in PhysicsNeMo?
 
@@ -24,8 +24,8 @@ model architecture can be applied to a specific problem.
 These are reference starting points for users to get started.
 
 You can find the list of built in model architectures
-[here](https://github.com/NVIDIA/modulus/tree/main/modulus/models) and
-[here](https://github.com/NVIDIA/modulus-sym/tree/main/modulus/sym/models)
+[here](https://github.com/NVIDIA/physicsnemo/tree/main/physicsnemo/models) and
+[here](https://github.com/NVIDIA/physicsnemo-sym/tree/main/physicsnemo/sym/models)
 
 ## What is the difference between PhysicsNeMo Core and Symbolic?
 
@@ -38,23 +38,23 @@ abstraction to compose a training loop from specification of the geometry, PDEs
 constraints like boundary conditions using simple symbolic APIs.
 So if you are familiar with PyTorch and want to train model from a dataset, you start
 with PhysicsNeMo core and you import PhysicsNeMo symbolic to bring in explicit domain knowledge.
-Please refer to the [DeepONet example](https://github.com/modulus/tree/main/examples/cfd/darcy_deeponet_physics)
+Please refer to the [DeepONet example](https://github.com/physicsnemo/tree/main/examples/cfd/darcy_deeponet_physics)
 that illustrates the concept.
 If you are an engineer or domain expert accustomed to using numerical solvers, you can
 use PhysicsNeMo Symbolic to define your problem at a higher level of abstraction. Please
-refer to the [Lid Driven cavity](https://docs.nvidia.com/deeplearning/modulus/modulus-sym/user_guide/basics/lid_driven_cavity_flow.html)
+refer to the [Lid Driven cavity](https://docs.nvidia.com/deeplearning/physicsnemo/physicsnemo-sym/user_guide/basics/lid_driven_cavity_flow.html)
 that illustrates the concept.
 
 ## What can I do if I dont see a PDE in PhysicsNeMo?
 
 PhysicsNeMo Symbolic provides a well documeted
-[example](https://docs.nvidia.com/deeplearning/modulus/modulus-sym/user_guide/foundational/1d_wave_equation.html#writing-custom-pdes-and-boundary-initial-conditions)
-that walks you through how to define a custom PDE. Please see the source [here](https://github.com/NVIDIA/modulus-sym/tree/main/modulus/sym/eq/pdes)
+[example](https://docs.nvidia.com/deeplearning/physicsnemo/physicsnemo-sym/user_guide/foundational/1d_wave_equation.html#writing-custom-pdes-and-boundary-initial-conditions)
+that walks you through how to define a custom PDE. Please see the source [here](https://github.com/NVIDIA/physicsnemo-sym/tree/main/physicsnemo/sym/eq/pdes)
 to see the built-in PDE implementation as an additional reference for your own implementation.
 
 ## What is the difference between the pip install and the container?
 
 There is no functional difference between the two. This is to simplify the ease of
 installing and setting up the PhysicsNeMo environment. Please refer to the
-[getting started guide](https://docs.nvidia.com/deeplearning/modulus/getting-started/index.html#modulus-with-docker-image-recommended)
+[getting started guide](https://docs.nvidia.com/deeplearning/physicsnemo/getting-started/index.html#physicsnemo-with-docker-image-recommended)
 on how to install using Pip or using the container.