Merge branch 'main' into structure

Author: santisoler

.github/pull_request_template.md

@@ -0,0 +1,48 @@
+<!-- 
+Thanks for contributing a pull request to SimPEG user tutorials!
+Remember to use a personal fork of SimPEG user tutorials to propose changes.
+
+Check out the stages of a pull request at
+https://docs.simpeg.xyz/content/getting_started/contributing/pull-requests.html
+
+Note that we are a team of volunteers and we appreciate your
+patience during the review process.
+
+Again, thanks for contributing!
+
+Feel free to remove lines from this template that do not apply to you pull request.
+-->
+
+#### Summary
+<!-- Add a summary of this Pull Request. Explain what it provides as tutorial material. -->
+
+#### PR Checklist
+* [ ] If this is a work in progress PR, set as a Draft PR
+* [ ] General
+    * [ ] Notebook is compatible with latest SimPEG release
+    * [ ] No deprecated functions and/or input arguments are being used
+    * [ ] Coding cells linted according to the [style guides](https://docs.simpeg.xyz/latest/content/getting_started/contributing/code-style.html).
+* [ ] Introduction is complete:
+    * [ ] Title and author added to notebook
+    * [ ] Admonitions for notebook difficulty and computational resources have been added
+    * [ ] Keywords list has been added
+    * [ ] Summary paragraph describing the tutorial has been added
+    * [ ] Learning objectives have been listed
+    * [ ] Hyperlinks to other tutorial notebooks added if necessary
+* [ ] For sections and subsections:
+    * [ ] A header and short summary of what is being done
+    * [ ] Links to API documentation added for all classes and functions that are used
+    * [ ] Newly introduced functionality is explained, or links are provided to relevant materials
+    * [ ] The approach taken when choosing hyperparameter values is explained. The use of ad hoc values without explanation is discouraged
+    * [ ] All figures are legible and rendered appropriately
+* [ ] Marked as ready for review (if this is was a draft PR), and converted to a pull request
+* [ ] Tagged ``@simpeg/simpeg-developers`` when ready for review
+
+
+#### Additional information
+<!--Any additional information you think is important.-->
+
+
+<!--
+Once all tests pass and the code has been reviewed and approved, it will be merged into main
+-->

.github/workflows/build.yml

@@ -18,10 +18,10 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Node
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: '20'
 
@@ -32,18 +32,25 @@ jobs:
       - name: Print MyST version
         run: myst --version
 
-      - name: Build website as static HTML
+      - name: Build website as static HTML (for PR)
+        if: github.event_name == 'pull_request'
+        run: |
+          echo "Building MyST website without setting BASE_URL"
+          myst build --html
+
+      - name: Build website as static HTML (for deploy)
+        if: github.event_name != 'pull_request'
         run: |
           echo "Building MyST website using BASE_URL=" $BASE_URL
           myst build --html
         env:
           BASE_URL: /${{ github.event.repository.name }}
 
       # Store the website as a build artifact so we can deploy it later
+      # or preview the website in a PR.
       - name: Upload HTML website as an artifact
-        # Only if not a pull request
-        if: success() && github.event_name != 'pull_request'
-        uses: actions/upload-artifact@v4
+        if: success()
+        uses: actions/upload-artifact@v6
         with:
           name: html-${{ github.sha }}
           path: _build/html
@@ -59,11 +66,11 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       # Fetch the built HTML from the build job
       - name: Download HTML artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           name: html-${{ github.sha }}
           path: _build/html

.github/workflows/check.yml

@@ -17,15 +17,15 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.PYTHON }}
 
       - name: Install required packages
-        run: pip install ruff nbqa
+        run: pip install ruff
 
       - name: Check style of notebooks
         run: make check

Makefile

@@ -1,29 +1,36 @@
 NOTEBOOKS_DIR=notebooks
 
-.PHONY: build run clean check format
+.PHONY: build run clean check check-style check-format format
 
 help:
 	@echo "Commands:"
 	@echo ""
-	@echo "  build   build Myst website (without running notebooks)"
-	@echo "  clean   clean output of Myst website"
-	@echo "  run     run all notebooks"
-	@echo "  check   lint notebooks with nbqa and ruff"
-	@echo "  format  autoformat notebooks with nbqa and ruff"
+	@echo "  build        build Myst website (without running notebooks)"
+	@echo "  clean        clean output of Myst website"
+	@echo "  run          run all notebooks"
+	@echo "  check        check notebooks style and format with ruff"
+	@echo "  check-style  check notebooks style with ruff"
+	@echo "  check-format check notebooks format with ruff"
+	@echo "  format       autoformat notebooks with ruff"
 	@echo ""
 
 
 build:
-	msyt build --html
+	myst build --html
 
 clean:
-	msyt clean --all
+	myst clean --all
 
 run:
 	jupyter nbconvert --to notebook --execute --inplace "${NOTEBOOKS_DIR}/**/*.ipynb"
 
-check:
-	nbqa ruff "${NOTEBOOKS_DIR}"
+check: check-format check-style
+
+check-style:
+	ruff check "${NOTEBOOKS_DIR}"
+
+check-format:
+	ruff format --check "${NOTEBOOKS_DIR}"
 
 format:
-	nbqa ruff --fix "${NOTEBOOKS_DIR}"
+	ruff format "${NOTEBOOKS_DIR}"

README.md

@@ -51,7 +51,7 @@ preview it. Follow the instructions that will be prompted by the command to see
 the website:
 
 ```bash
-msyt start
+myst start
 ```
 
 #### Build only
@@ -60,7 +60,7 @@ The following command will build the website and store the HTML files in
 a new `_build` folder:
 
 ```bash
-msyt build --html
+myst build --html
 ```
 
 #### Clean cached builds
@@ -115,24 +115,31 @@ jupyter nbconvert --to notebook --execute --inplace notebooks/**/*.ipynb
 
 ## Check style of notebooks
 
-We can check the code style of our notebooks using [`ruff`][ruff] and
-[`nbqa`][nbqa]. Simply run the following command to check the style of the
-notebooks:
+We can check the code style of our notebooks using [`ruff`][ruff].
+Simply run the following command to check the style of the notebooks:
 
 ```bash
-nbqa ruff notebooks
+ruff check notebooks
+```
+
+You can run the following that the notebooks are correctly formatted:
+
+```bash
+ruff format --check notebooks
 ```
 
 And run this to autoformat them:
 
 ```bash
-nbqa ruff --fix notebooks
+ruff format --fix notebooks
 ```
 
 Alternatively, you can use the targets we have in the `Makefile`, like `make
 check` and `make format`. Read more information about the available targets
 by running `make help`.
 
+[ruff]: https://astral.sh/ruff
+
 ## License
 
 All text and figures are licensed under a

assets/05-dcr/inv_dcr_3d_files.tar.gz

@@ -2,19 +2,18 @@ name: simpeg-user-tutorials
 channels:
   - conda-forge
 dependencies:
-  - python=3.10.*
+  - python=3.13.*
   # Myst requirements
   - nodejs>18
   - mystmd
   # Notebook requirements
   - jupyter
   - jupyterlab-myst
   - nbconvert
-  - simpeg==0.23.*
-  - discretize==0.11.*
+  - simpeg==0.25.*
+  - discretize==0.12.*
   - choclo==0.3.*
-  - scikit-learn
+  - scikit-learn==1.7.*
   - pymatsolver
-  # Code quality
-  - nbqa
+  # Code style
   - ruff

assets/06-ip/inv_ip_3d_files.tar.gz

@@ -10,7 +10,7 @@ SimPEG user tutorials is the place for those who have [installed SimPEG](https:/
 
 
 :::{caution} Caution
-These user tutorials are meant to be run with **SimPEG v0.23**.
+These user tutorials are meant to be run with **SimPEG v0.25**.
 Please, make sure you have this version installed.
 :::
 
@@ -106,3 +106,10 @@ Requires moderate computational resources. Run-times may exceed several minutes
 The computational resources required to execute this notebook exceed those provided by standard laptop computers. To execute the notebook, please deploy to a cluster computing environment.
 ```
 
+Want to Add a Tutorial?
+-----------------------
+
+Please visit the [Contributing to User Tutorials](notebooks/contributing_index.md) page to find out how you can add a tutorial.
+
+
+

environment.yml

@@ -17,6 +17,7 @@ project:
       - name: Devin Cowan
         id: devincowan
         affiliations: ubc
+        orcid: 0000-0002-0089-402X
         roles:
           - writing
           - editing
@@ -115,6 +116,11 @@ project:
       children:
         - file: notebooks/pgi/plot_inv_1_joint_pf_pgi_full_info_tutorial.ipynb
         - file: notebooks/pgi/plot_inv_2_joint_pf_pgi_no_info_tutorial.ipynb
+    - file: notebooks/contributing_index.md
+      children:
+        - file: notebooks/contributing/build_website.md
+        - file: notebooks/contributing/formatting.md
+        - file: notebooks/contributing/pull_request.md
 
 site:
   template: book-theme