MiraGeoscience · domfournier · Mar 6, 2025 · Mar 6, 2025 · Mar 6, 2025 · Mar 6, 2025
diff --git a/.ci/azure/docs.yml b/.ci/azure/docs.yml
@@ -5,7 +5,7 @@ jobs:
     pool:
       vmImage: ubuntu-latest
     variables:
-      python.version: "3.10"
+      python.version: "3.11"
     timeoutInMinutes: 240
     steps:
       # Checkout simpeg repo.

diff --git a/.ci/azure/pypi.yml b/.ci/azure/pypi.yml
@@ -12,7 +12,7 @@ jobs:
 
       - task: UsePythonVersion@0
         inputs:
-          versionSpec: "3.10"
+          versionSpec: "3.11"
         displayName: "Setup Python"
 
       - bash: |
@@ -57,7 +57,7 @@ jobs:
 
       - task: UsePythonVersion@0
         inputs:
-          versionSpec: "3.10"
+          versionSpec: "3.11"
         displayName: "Setup Python"
 
       - bash: |

diff --git a/.ci/azure/setup_env.sh b/.ci/azure/setup_env.sh
@@ -2,10 +2,17 @@
 set -ex #echo on and exit if any line fails
 
 # TF_BUILD is set to True on azure pipelines.
-is_azure=$(${TF_BUILD:-false} | tr '[:upper:]' '[:lower:]')
+is_azure=$(echo "${TF_BUILD:-false}" | tr '[:upper:]' '[:lower:]')
 
 if ${is_azure}
 then
+  # Add conda-forge as channel
+  conda config --add channels conda-forge
+  # Remove defaults channels
+  # (both from ~/.condarc and from /usr/share/miniconda/.condarc)
+  conda config --remove channels defaults
+  conda config --remove channels defaults --system
+  # Update conda
   conda update --yes -n base conda
 fi
 
@@ -30,4 +37,4 @@ echo "Conda Environment:"
 conda list
 
 echo "Installed SimPEG version:"
-python -c "import simpeg; print(simpeg.__version__)"
+python -c "import simpeg; print(simpeg.__version__)"
diff --git a/.ci/azure/test.yml b/.ci/azure/test.yml
@@ -1,6 +1,6 @@
 parameters:
   os : ['ubuntu-latest']
-  py_vers: ['3.10']
+  py_vers: ['3.11']
   test: ['tests/em',
          'tests/base tests/flow tests/seis tests/utils',
          'tests/meta',

diff --git a/.ci/environment_test.yml b/.ci/environment_test.yml
@@ -3,12 +3,13 @@ channels:
   - conda-forge
 dependencies:
   - numpy>=1.22
-  - scipy>=1.8
+  - scipy>=1.12
   - pymatsolver>=0.3
   - matplotlib-base
   - discretize>=0.11
   - geoana>=0.7
   - libdlf
+  - typing_extensions
 
 # optional dependencies
   - dask
@@ -24,6 +25,8 @@ dependencies:
   - sphinx
   - sphinx-gallery>=0.1.13
   - sphinxcontrib-apidoc
+  - sphinx-reredirects
+  - sphinx-design
   - pydata-sphinx-theme
   - nbsphinx
   - numpydoc
@@ -43,4 +46,4 @@ dependencies:
 # PyPI uploading
   - wheel
   - twine
-  - build
+  - python-build
diff --git a/.github/ISSUE_TEMPLATE/bug-report.yml b/.github/ISSUE_TEMPLATE/bug-report.yml
@@ -1,7 +1,7 @@
 name: Bug report
 description: Report a bug in SimPEG.
 title: "BUG: <Please write a comprehensive title after the 'BUG: ' prefix>"
-labels: [Bug]
+labels: ["bug"]
 
 body:
 - type: markdown
@@ -46,6 +46,7 @@ body:
     description: >
       Please include the output from `simpeg.Report()` to describe your system for us.
       Paste the output from `from simpeg import Report; print(Report())` below.
+    render: shell
   validations:
     required: true
 

diff --git a/.github/zizmor.yml b/.github/zizmor.yml
@@ -0,0 +1,17 @@
+# Zizmor configuration
+# --------------------
+#
+# This file configures zizmor. This is not a workflow that gets run in GitHub
+# Actions.
+#
+# References: https://woodruffw.github.io/zizmor/configuration
+
+rules:
+  unpinned-uses:
+    config:
+      policies:
+        # Mimic default behaviour: official actions can get pinned by tag.
+        actions/*: ref-pin
+        # Allow to use tags to pin reviewdog actions.
+        reviewdog/action-black: ref-pin
+        reviewdog/action-flake8: ref-pin
diff --git a/.gitignore b/.gitignore
@@ -47,8 +47,8 @@ docs/_build/
 docs/warnings.txt
 docs/content/api/generated/*
 .DS_Store
-docs/content/examples/*
-docs/content/tutorials/*
+docs/content/user-guide/examples/*
+docs/content/user-guide/tutorials/*
 docs/modules/*
 docs/sg_execution_times.rst
 .vscode/*

diff --git a/CITATION.rst b/CITATION.rst
@@ -1,13 +1,17 @@
+=============
 Citing SimPEG
--------------
+=============
 
-There is a `paper about SimPEG <http://dx.doi.org/10.1016/j.cageo.2015.09.015>`_, if you use this code, please help our scientific visibility by citing our work!
+There is a paper about SimPEG! If you are using this library in your research,
+we greatly appreciate that the software gets cited!
 
 
-    Cockett, R., Kang, S., Heagy, L. J., Pidlisecky, A., & Oldenburg, D. W. (2015). SimPEG: An open source framework for simulation and gradient based parameter estimation in geophysical applications. Computers & Geosciences.
+    Cockett, R., Kang, S., Heagy, L. J., Pidlisecky, A., & Oldenburg, D. W.
+    (2015). SimPEG: An open source framework for simulation and gradient based
+    parameter estimation in geophysical applications. Computers & Geosciences.
 
 
-BibTex:
+Here is a Bibtex entry to make things easier if you’re using Latex:
 
 .. code::
 
@@ -19,3 +23,24 @@ BibTex:
       publisher={Elsevier}
     }
 
+Electromagnetics
+----------------
+
+If you are using the :mod:`simpeg.electromagnetics` module, please also cite:
+
+    Lindsey J. Heagy, Rowan Cockett, Seogi Kang, Gudni K. Rosenkjaer, Douglas W. Oldenburg, A framework for simulation and inversion in electromagnetics, Computers & Geosciences, Volume 107, 2017, Pages 1-19, ISSN 0098-3004, http://dx.doi.org/10.1016/j.cageo.2017.06.018.
+
+Here is a Bibtex entry to make things easier if you’re using Latex:
+
+.. code::
+
+    @article{heagy2017,
+      title={A framework for simulation and inversion in electromagnetics},
+      author={Lindsey J. Heagy and Rowan Cockett and Seogi Kang and Gudni K. Rosenkjaer and Douglas W. Oldenburg},
+      journal={Computers & Geosciences},
+      volume={107},
+      pages={1 - 19},
+      year={2017},
+      issn={0098-3004},
+      doi={http://dx.doi.org/10.1016/j.cageo.2017.06.018}
+    }
diff --git a/README.rst b/README.rst
@@ -48,7 +48,7 @@ The vision is to create a package for finite volume simulation with applications
 
 You are welcome to join our forum and engage with people who use and develop SimPEG at: https://simpeg.discourse.group/.
 
-Weekly meetings are open to all. They are generally held on Wednesdays at 10:30am PDT. Please see the calendar (`GCAL <https://calendar.google.com/calendar/b/0?cid=ZHVhamYzMWlibThycWdkZXM5NTdoYXV2MnNAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ>`_, `ICAL <https://calendar.google.com/calendar/ical/duajf31ibm8rqgdes957hauv2s%40group.calendar.google.com/public/basic.ics>`_) for information on the next meeting.
+Weekly meetings are open to all. They are generally held on Wednesdays at 3:00 PM Pacific Time. Please see the calendar (`GCAL <https://calendar.google.com/calendar/b/0?cid=ZHVhamYzMWlibThycWdkZXM5NTdoYXV2MnNAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ>`_, `ICAL <https://calendar.google.com/calendar/ical/duajf31ibm8rqgdes957hauv2s%40group.calendar.google.com/public/basic.ics>`_) for information on the next meeting.
 
 Overview Video
 ==============
@@ -120,9 +120,8 @@ Meetings
 SimPEG hosts weekly meetings for users to interact with each other,
 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
+Currently our meetings are held every Wednesday at 3:00 PM Pacific Time.
+Find more info on our
 `Mattermost <https://mattermost.softwareunderground.org/simpeg>`_.
 
 

diff --git a/docs/Makefile b/docs/Makefile
@@ -43,8 +43,8 @@ help:
 clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf content/api/generated/
-	rm -rf content/examples/
-	rm -rf content/tutorials/
+	rm -rf content/user-guide/examples/
+	rm -rf content/user-guide/tutorials/
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html -j auto

diff --git a/docs/_static/versions.json b/docs/_static/versions.json
@@ -4,11 +4,16 @@
         "url": "https://docs.simpeg.xyz/dev/"
     },
     {
-        "name": "v0.23.0 (latest)",
-        "version": "0.23.0",
-        "url": "https://docs.simpeg.xyz/v0.23.0/",
+        "name": "v0.24.0 (latest)",
+        "version": "0.24.0",
+        "url": "https://docs.simpeg.xyz/v0.24.0/",
         "preferred": true
     },
+    {
+        "name": "v0.23.0",
+        "version": "0.23.0",
+        "url": "https://docs.simpeg.xyz/v0.23.0/"
+    },
     {
         "name": "v0.22.2",
         "version": "0.22.2",

diff --git a/docs/conf.py b/docs/conf.py
@@ -10,7 +10,7 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
-
+from pathlib import Path
 import sys
 import os
 from sphinx_gallery.sorting import FileNameSortKey
@@ -44,11 +44,13 @@
     "sphinx.ext.coverage",
     "sphinx.ext.doctest",
     "sphinx.ext.extlinks",
+    "sphinx_design",
     "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx_gallery.gen_gallery",
     "sphinx.ext.todo",
     "matplotlib.sphinxext.plot_directive",
+    "sphinx_reredirects",
 ]
 
 # Autosummary pages will be generated by sphinx-autogen instead of sphinx-build
@@ -98,8 +100,8 @@
 
 linkcheck_ignore = [
     r"https://github.com/simpeg/simpeg*",
-    "/content/examples/*",
-    "/content/tutorials/*",
+    "/content/user-guide/examples/*",
+    "/content/user-guide/tutorials/*",
     r"https://www.pardiso-project.org",
     r"https://docs.github.com/*",
     # GJI refuses the connexion during the check
@@ -296,6 +298,7 @@ def linkcode_resolve(domain, info):
         "json_url": "https://docs.simpeg.xyz/latest/_static/versions.json",
     },
     "show_version_warning_banner": True,
+    "navigation_with_keys": True,
 }
 
 html_logo = "images/simpeg-logo.png"
@@ -464,7 +467,9 @@ def linkcode_resolve(domain, info):
 ]
 
 tutorial_dirs = glob.glob("../tutorials/[!_]*")
-tut_gallery_dirs = ["content/tutorials/" + os.path.basename(f) for f in tutorial_dirs]
+tut_gallery_dirs = [
+    "content/user-guide/tutorials/" + os.path.basename(f) for f in tutorial_dirs
+]
 
 # Scaping images to generate on website
 from plotly.io._sg_scraper import plotly_sg_scraper
@@ -475,7 +480,7 @@ def linkcode_resolve(domain, info):
 sphinx_gallery_conf = {
     # path to your examples scripts
     "examples_dirs": ["../examples"] + tutorial_dirs,
-    "gallery_dirs": ["content/examples"] + tut_gallery_dirs,
+    "gallery_dirs": ["content/user-guide/examples"] + tut_gallery_dirs,
     "within_subsection_order": FileNameSortKey,
     "filename_pattern": "\.py",
     "backreferences_dir": "content/api/generated/backreferences",
@@ -531,3 +536,51 @@ def linkcode_resolve(domain, info):
     ("py:class", "builtins.complex"),
     ("py:meth", "__call__"),
 ]
+
+
+# Configure redirects
+# -------------------
+# Redirect some pages to support old links
+OLD_FILES_FNAME = Path(__file__).parent.resolve() / "old-docs-files.txt"
+MAPS = {
+    "content/tutorials": "content/user-guide/tutorials",
+    "content/examples": "content/user-guide/examples",
+    "content/getting_started": "content/user-guide/getting-started",
+}
+IGNORE = ["content/getting_started/index.html", "content/user_guide.html"]
+
+
+def _get_source_target(old_fname: str) -> tuple[str, str]:
+    for old_dir, new_dir in MAPS.items():
+        if old_fname.startswith(old_dir):
+            source = old_fname.removesuffix(".html")
+            n_parents = len([p for p in Path(old_fname).parents if p != Path(".")])
+            target = "../" * n_parents + old_fname.replace(old_dir, new_dir, 1)
+            return source, target
+    raise ValueError()
+
+
+def build_redirects():
+    """
+    Build redirects dictionary for sphinx-reredirects.
+    """
+    redirects = {}
+    with OLD_FILES_FNAME.open(mode="r") as f:
+        for line in f:
+            if line.startswith("#"):
+                continue
+            old_fname = line.strip()
+            if old_fname in IGNORE:
+                continue
+            source, target = _get_source_target(old_fname)
+            redirects[source] = target
+    return redirects
+
+
+redirects = build_redirects()
+redirects.update(
+    {
+        "content/getting_started/index": "../../content/user-guide/index.html",
+        "content/user_guide": "../content/user-guide/index.html",
+    }
+)
diff --git a/docs/content/api/index.rst b/docs/content/api/index.rst
@@ -32,6 +32,15 @@ Regularizations
 
   simpeg.regularization
 
+Optimizers
+----------
+Optimizers used within SimPEG inversions.
+
+.. toctree::
+  :maxdepth: 2
+
+  simpeg.optimization
+
 Directives
 ----------
 .. toctree::
@@ -41,7 +50,6 @@ Directives
 
 Utilities
 ---------
-
 Classes and functions for performing useful operations.
 
 .. toctree::

diff --git a/docs/content/api/simpeg.optimization.rst b/docs/content/api/simpeg.optimization.rst
@@ -0,0 +1 @@
+.. automodule:: simpeg.optimization
diff --git a/docs/content/getting_started/index.rst b/docs/content/getting_started/index.rst