Update to SimPEG 0.21.1 (before changes to simpeg lowercase)

.azure-pipelines/matrix.yml

@@ -50,6 +50,13 @@ jobs:
               pytest ${{ test }} -v --cov-config=.coveragerc --cov=SimPEG --cov-report=xml --cov-report=html -W ignore::DeprecationWarning
             displayName: 'Testing ${{ test }}'
 
+          - task: PublishPipelineArtifact@1
+            inputs:
+              targetPath: $(Build.SourcesDirectory)/docs/_build/html
+              artifactName: html_docs
+            displayName: 'Publish documentation artifact'
+            condition: eq('${{ test }}', 'tests/docs -s -v')
+
           - script: |
               curl -Os https://uploader.codecov.io/latest/linux/codecov
               chmod +x codecov

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -7,7 +7,7 @@ body:
 - type: markdown
   attributes:
     value: >
-      Thanks for your use of SimPEG and for taking the time to report a bug! Please
+      Thanks for using SimPEG and taking the time to report a bug! Please
       first double check that there is not already a bug report on this issue by
       searching through the existing bugs.
 
@@ -19,11 +19,11 @@ body:
 
 - type: textarea
   attributes:
-    label: "Reproducable code example:"
+    label: "Reproducible code example:"
     description: >
       Please submit a small, but complete, code sample that reproduces the
       bug or missing functionality. It should be able to be copy-pasted
-      into a Python interpreter and ran as-is.
+      into a Python interpreter and run as-is.
     placeholder: |
       import SimPEG
       << your code here >>
@@ -58,4 +58,4 @@ body:
     placeholder: |
       << your explanation here >>
   validations:
-    required: false
+    required: false

.github/ISSUE_TEMPLATE/config.yml

@@ -3,5 +3,5 @@ contact_links:
     url: https://simpeg.discourse.group/
     about: "If you have a question on how to use SimPEG, please submit them to our discourse page."
   - name: Development-related matters
-    url: http://slack.simpeg.xyz/
-    about: "If you would like to discuss SimPEG, any geophysics related problems, or need help from the SimPEG team, get in touch with us on slack."
+    url: https://mattermost.softwareunderground.org/simpeg
+    about: "If you would like to discuss SimPEG, any geophysics related problems, or need help from the SimPEG team, get in touch with us on Mattermost."

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -6,10 +6,11 @@ body:
 - type: markdown
   attributes:
     value: >
-      If you'd like to request a new feature in SimPEG, or suggest changes in the
-      functionality of certain functions, we recommend getting in touch with the
-      developers on [slack](https://slack.simpeg.xyz), in addition to opening an
-      issue or pull request here.
+      If you'd like to request a new feature in SimPEG, or suggest changes in
+      the functionality of certain functions, we recommend getting in touch
+      with the developers on
+      [Mattermost](https://mattermost.softwareunderground.org/simpeg), in
+      addition to opening an Issue or Pull Request here.
       You can also check out our
       [Contributor Guide](https://docs.simpeg.xyz/content/getting_started/contributing/index.html)
       if you need more information.

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -0,0 +1,151 @@
+---
+name: Release checklist
+about: "Maintainers only: Checklist for making a new release"
+title: "Release vX.Y.Z"
+labels: "maintenance"
+assignees: ""
+---
+
+<!-- Optional -->
+
+**Target date:** YYYY/MM/DD
+
+## Generate release notes
+
+### Autogenerate release notes with GitHub
+
+- [ ] Generate a draft for a new Release in GitHub.
+- [ ] Create a new tag for it (the version number with a leading `v`).
+- [ ] Generate release notes automatically.
+- [ ] Copy those notes and paste them into a `notes.md` file.
+- [ ] Discard the draft (we'll generate a new one later on).
+
+### Add release notes to the docs
+
+- [ ] Convert the Markdown file to RST with: `pandoc notes.md -o notes.rst`.
+- [ ] Generate list of contributors from the release notes with:
+  ```bash
+  grep -Eo "@[[:alnum:]-]+" notes.rst | sort -u | sed -E 's/^/* /'
+  ```
+  Paste the list into the file under a new `Contributors` category.
+- [ ] Check if every contributor that participated in the release is in the
+  list. Generate a list of authors and co-authors from the git log with (update
+  the `last_release`):
+  ```bash
+  export last_release="v0.20.0"
+  git shortlog HEAD...$last_release -sne > contributors
+  git log HEAD...$last_release | grep "Co-authored-by" | sed 's/Co-authored-by://' | sed 's/^[[:space:]]*/ /' | sort | uniq -c | sort -nr | sed 's/^ //' >> contributors
+  sort -rn contributors
+  ```
+- [ ] Transform GitHub handles into links to their profiles:
+  ```bash
+  sed -Ei 's/@([[:alnum:]-]+)/`@\1 <https:\/\/github.com\/\1>`__/' notes.rst
+  ```
+- [ ] Copy the content of `notes.rst` to a new file
+  `docs/content/release/<version>-notes.rst`.
+- [ ] Edit the release notes file, following the template below and the
+  previous release notes.
+- [ ] Add the new release notes to the list in `docs/content/release/index.rst`.
+- [ ] Open a PR with the new release notes.
+- [ ] Manually view the built documentation by downloading the Azure `html_doc`
+  artifact and check for formatting and errors.
+- [ ] Merge that PR
+
+
+<details>
+<summary>Template for release notes:</summary>
+
+```rst
+.. _<VERSION>_notes:
+
+===========================
+SimPEG <VERSION> Release Notes
+===========================
+
+MONTH DAYth, YEAR
+
+.. contents:: Highlights
+    :depth: 3
+
+Updates
+=======
+
+New features
+------------
+
+..
+    list new features under subheadings, include link to related PRs
+
+Documentation
+-------------
+
+..
+    list improvements to documentation
+
+Bugfixes
+--------
+
+..
+    list bugfixes, include link to related PRs
+
+Breaking changes
+----------------
+
+..
+    list breaking changes introduced in this new release, include link to
+    releated PRs
+
+Contributors
+============
+
+..
+    paste list of contributors that was generated in `notes.rst`
+
+Pull Requests
+=============
+
+..
+    paste list of PRs that were copied to `notes.rst`
+```
+
+</details>
+
+
+## Make the new release
+
+- [ ] Draft a new GitHub Release
+- [ ] Create a new tag for it (the version number with a leading `v`).
+- [ ] Target the release on `main` or on a particular commit from `main`
+- [ ] Generate release notes automatically.
+- [ ] Publish the release
+
+## Extra tasks
+
+After publishing the release, Azure will automatically push the new version to
+PyPI, and build and deploy the docs. You can check the progress of these tasks
+in: https://dev.azure.com/simpeg/simpeg/_build
+
+After they finish:
+
+- [ ] Check the new version is available in PyPI: https://pypi.org/project/SimPEG/
+- [ ] Check the new documentation is online: https://docs.simpeg.xyz
+
+For the new version to be available in conda-forge, we need to update the
+[conda-forge/simpeg-feedstock](https://github.com/conda-forge/simpeg-feedstock)
+repository. Within the same day of the release a new PR will be automatically
+open in that repository. So:
+
+- [ ] Follow the steps provided in the checklist in that PR and merge it.
+- [ ] Make sure the new version is available through conda-forge: https://anaconda.org/conda-forge/simpeg
+
+Lastly, we would need to update the SimPEG version used in
+[`simpeg/user-tutorials`](https://github.com/simpeg/user-tutorials) and rerun
+its notebooks:
+
+- [ ] Open issue in
+  [`simpeg/user-tutorials`](https://github.com/simpeg/user-tutorials) for
+  rerunning the notebooks using the new released version of SimPEG
+
+Finally:
+
+- [ ] Close this issue

.github/workflows/pull_request.yml

@@ -0,0 +1,58 @@
+name : Reviewdog PR Annotations
+on: [pull_request_target]
+
+jobs:
+  flake8:
+    runs-on: ubuntu-latest
+    name: Flake8 check
+    steps:
+      - name: Checkout target repository source
+        uses: actions/checkout@v4
+
+      - name: Setup Python env
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies to run the flake8 checks
+        run: pip install -r requirements_style.txt
+
+      - name: checkout pull request source
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          path: pr_source
+
+      - name: flake8 review
+        uses: reviewdog/action-flake8@v3
+        with:
+          workdir: pr_source
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          reporter: github-pr-review
+
+  black:
+    name: Black check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout target repository source
+        uses: actions/checkout@v4
+
+      - name: Setup Python env
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies to run the black checks
+        run: pip install -r requirements_style.txt
+
+      - name: checkout pull request source
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          path: 'pr_source'
+
+      - uses: reviewdog/action-black@v3
+        with:
+          workdir: 'pr_source'
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          reporter: github-pr-review

.gitignore

@@ -49,6 +49,7 @@ docs/content/api/generated/*
 docs/content/examples/*
 docs/content/tutorials/*
 docs/modules/*
+docs/sg_execution_times.rst
 .vscode/*
 
 # paths to where data are downloaded

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.3.0
     hooks:
       - id: black
         language_version: python3

AUTHORS.rst

@@ -18,4 +18,11 @@
 - Thibaut Astic, (`@thast <https://github.com/thast/>`_)
 - Michael Mitchell, (`@micmitch <https://github.com/micmitch/>`_)
 - I-Kang Ding, (`@ikding <https://github.com/ikding/>`_)
-- Richard Scott (`@bluetyson <https://github.com/bluetyson/>`_)
+- Richard Scott, (`@bluetyson <https://github.com/bluetyson/>`_)
+- Xiaolong Wei, (`@xiaolongw1223 <https://github.com/xiaolongw1223>`_)
+- Santiago Soler, (`@santisoler <https://github.com/santisoler>`_)
+- Nick Williams, (`@nwilliams-kobold <https://github.com/nwilliams-kobold>`_)
+- John Weis, (`@johnweis0480 <https://github.com/johnweis0480>`_)
+- Kalen Martens, (`@kalen-sj <https://github.com/kalen-sj>`_)
+- Williams A. Lima (`@ghwilliams <https://github.com/ghwilliams>`_)
+- Ying Hu, (`@YingHuuu <https://github.com/YingHuuu>`_)

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2013-2023 SimPEG Developers
+Copyright (c) 2013-2024 SimPEG Developers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.rst

@@ -30,8 +30,8 @@ SimPEG
 .. image:: https://img.shields.io/discourse/users?server=http%3A%2F%2Fsimpeg.discourse.group%2F
     :target: https://simpeg.discourse.group/
 
-.. image:: https://img.shields.io/badge/Slack-simpeg-4A154B.svg?logo=slack
-    :target: http://slack.simpeg.xyz
+.. image:: https://img.shields.io/badge/simpeg-purple?logo=mattermost&label=Mattermost
+    :target: https://mattermost.softwareunderground.org/simpeg
 
 .. image:: https://img.shields.io/badge/Youtube%20channel-GeoSci.xyz-FF0000.svg?logo=youtube
     :target: https://www.youtube.com/channel/UCBrC4M8_S4GXhyHht7FyQqw
@@ -109,7 +109,8 @@ Questions
 If you have a question regarding a specific use of SimPEG, the fastest way
 to get a response is by posting on our Discourse discussion forum:
 https://simpeg.discourse.group/. Alternatively, if you prefer real-time chat,
-you can join our slack group at http://slack.simpeg.xyz.
+you can join our Mattermost Team at
+https://mattermost.softwareunderground.org/simpeg.
 Please do not create an issue to ask a question.
 
 
@@ -121,7 +122,8 @@ for developers to discuss upcoming changes to the code base, and for
 discussing topics related to geophysics in general.
 Currently our meetings are held every Wednesday, alternating between
 a mornings (10:30 am pacific time) and afternoons (3:00 pm pacific time)
-on even numbered Wednesdays. Find more info on our `slack <http://slack.simpeg.xyz>`_.
+on even numbered Wednesdays. Find more info on our
+`Mattermost <https://mattermost.softwareunderground.org/simpeg>`_.
 
 
 Links
@@ -134,8 +136,8 @@ Forums:
 https://simpeg.discourse.group/
 
 
-Slack (real time chat):
-http://slack.simpeg.xyz
+Mattermost (real time chat):
+https://mattermost.softwareunderground.org/simpeg
 
 
 Documentation:

SimPEG/__init__.py

@@ -80,6 +80,7 @@
   maps.InjectActiveEdges
   maps.MuRelative
   maps.LogMap
+  maps.LogisticSigmoidMap
   maps.ParametricBlock
   maps.ParametricCircleMap
   maps.ParametricEllipsoid

SimPEG/base/pde_simulation.py

@@ -16,6 +16,9 @@ def __inner_mat_mul_op(M, u, v=None, adjoint=False):
                 # u has multiple fields
                 if v.ndim == 1:
                     v = v[:, None]
+                if adjoint and v.shape[1] != u.shape[1] and v.shape[1] > 1:
+                    # make sure v is a good shape
+                    v = v.reshape(u.shape[0], -1, u.shape[1])
             else:
                 if v.ndim > 1:
                     u = u[:, None]