Merge pull request #125 from MiraGeoscience/GEOPY-2522

GEOPY-2522: Update simpeg fork to 0.25

Author: domfournier

.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.

.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: |

.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__)"

.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',

.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
+  - discretize>=0.12
+  - geoana>=0.8.1
   - 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

.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
 

.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

.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/*

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}
+    }

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>`_.