Merge 5c5fd74 into 4305fe8

emsig · Mar 6, 2021 · 2f67694 · 2f67694
2 parents 4305fe8 + 5c5fd74
commit 2f67694
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -44,7 +44,7 @@ jobs:
           - python-version: 3.8
             name: plain
             os: ubuntu
-            conda: "'discretize<0.6'"  # Check discretize backwards comp.
+            conda: ""
           - python-version: 3.8
             name: full
             os: ubuntu

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,18 @@
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: []
+
+# Optionally set the version of Python and requirements required to build your
+# docs
+python:
+  version: 3.8
+  install:
+    - requirements: requirements-dev.txt
+    - method: pip
+      path: .
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,8 +2,44 @@ Changelog
 #########
 
 
-recent versions
-"""""""""""""""
+1.x-Series
+""""""""""
+
+
+latest: towards v1.0
+--------------------
+
+- ``Simulation``:
+
+  - ``name`` is new optional.
+  - New optional keyword ``info``.
+
+- ``Survey``:
+
+  - ``frequencies`` is new a dict just like ``sources`` and ``receivers``.
+  - ``sources`` and ``receivers`` must be tuples or dicts; lists are no longer
+    permitted. TODO: This will probably reduce to dicts only.
+  - Has no attribute ``observed`` any longer; access it just like any other
+    data through ``Survey.data.observed``.
+  - ``name`` is new optional.
+  - New optional keywords ``date`` and ``info``.
+  - ``noise_floor`` and ``relative_error`` are new stored as data array if they
+    are not floats.
+  - The keyword ``fixed`` has been dropped. To simulate fixed surveys define
+    the receivers with a relative offset to the source, instead of absolute
+    coordinates.
+  - ``data`` can be a dict containing many data set.
+
+- ``Dipole``:
+
+  - No ``name`` parameter any longer.
+
+
+- Removed all deprecated features.
+
+
+0.x-Series
+""""""""""
 
 
 v0.17.0: Magnetics in Simulation
@@ -121,9 +157,6 @@ v0.16.0: Arbitrarily shaped sources
   ``map_coordinates``.
 
 
-v0.11.0 - v0.15.3
-"""""""""""""""""
-
 v0.15.3: Move to EMSiG
 ----------------------
 
@@ -518,9 +551,6 @@ were removed, however.
   - Fixed ``io`` for ``SourceField``, that was not implemented properly.
 
 
-v0.8.0 - v0.10.1
-""""""""""""""""
-
 *v0.10.1* : Zero Source
 -----------------------
 
@@ -755,9 +785,6 @@ v0.8.0 - v0.10.1
     ``utils.get_stretched_h``.
 
 
-v0.1.0 - v0.7.1
-"""""""""""""""
-
 *v0.7.1* : JOSS article
 -----------------------
 

diff --git a/MAINTENANCE.rst b/MAINTENANCE.rst
@@ -1,5 +1,5 @@
-Maintainers Guide
-=================
+Development
+===========
 
 
 Making a release

diff --git a/docs/_static/style.css b/docs/_static/style.css
diff --git a/docs/code-cli.rst → docs/api_reference/code-cli.rst b/docs/code-cli.rst → docs/api_reference/code-cli.rst
diff --git a/docs/code-msaf.rst → docs/api_reference/code-msaf.rst b/docs/code-msaf.rst → docs/api_reference/code-msaf.rst
diff --git a/docs/code-opt.rst → docs/api_reference/code-opt.rst b/docs/code-opt.rst → docs/api_reference/code-opt.rst
diff --git a/docs/code-sas.rst → docs/api_reference/code-sas.rst b/docs/code-sas.rst → docs/api_reference/code-sas.rst
diff --git a/docs/code-solv.rst → docs/api_reference/code-solv.rst b/docs/code-solv.rst → docs/api_reference/code-solv.rst
diff --git a/docs/code-utio.rst → docs/api_reference/code-utio.rst b/docs/code-utio.rst → docs/api_reference/code-utio.rst
diff --git a/docs/api_reference/index.rst b/docs/api_reference/index.rst
@@ -0,0 +1,16 @@
+.. _api-reference:
+
+=============
+API reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API reference
+
+   code-solv
+   code-msaf
+   code-sas
+   code-opt
+   code-utio
+   code-cli
diff --git a/docs/changelog.rst b/docs/changelog.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,7 +20,6 @@
 # Numpydoc settings
 numpydoc_show_class_members = False
 numfig = True
-numfig_format = {'figure': 'Figure %s:'}
 
 # Todo settings
 todo_include_todos = True
@@ -48,7 +47,7 @@
 
 # General information about the project.
 project = 'emg3d'
-copyright = u'2018-{}, The emg3d Developers.'.format(time.strftime("%Y"))
+copyright = f'2018-{time.strftime("%Y")}, The emg3d Developers.'
 author = 'The emg3d Developers'
 
 # |version| and |today| tags (|release|-tag is not used).
@@ -63,41 +62,26 @@
 pygments_style = 'friendly'
 
 # ==== 3. HTML settings ====
-html_theme = 'sphinx_rtd_theme'
-html_theme_options = {
-    'logo_only': True,
-    'display_version': True,
-    'prev_next_buttons_location': 'both',
-}
+html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
 html_logo = '_static/logo-emg3d-cut.svg'
 html_favicon = '_static/favicon.ico'
-html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'searchbox.html',
-    ]
+
+html_theme_options = {
+  "github_url": "https://github.com/emsig/emg3d",
+  "external_links": [
+      {"name": "EMSiG", "url": "https://emsig.github.io"},
+  ],
+  "use_edit_page_button": True,
 }
 
 html_context = {
-    'menu_links_name': 'Links',
-    'menu_links': [
-        ('<i class="fa fa-link fa-fw"></i> Website',
-         'https://emsig.github.io'),
-        ('<i class="fa fa-github fa-fw"></i> Source Code',
-         'https://github.com/emsig/emg3d'),
-    ],
+    "github_user": "emsig",
+    "github_repo": "emg3d",
+    "github_version": "master",
+    "doc_path": "docs",
 }
 
-htmlhelp_basename = 'emg3ddoc'
-
-
-# -- CSS fixes --
-def setup(app):
-    app.add_css_file("style.css")
-
-
 # ==== 4. linkcheck ====
 
 # Papers from academic.oup results in a 104 error

diff --git a/docs/credits.rst b/docs/credits.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -11,28 +11,9 @@ Version: |version| ~ Date: |today|
 
 .. toctree::
    :maxdepth: 2
-   :hidden:
    :caption: User Manual
 
-   usage
-   mgwhat
-   theory
-   cpu_and_ram
-   cli
+   user_guide/index
    gallery
-   references
-   credits
-   changelog
+   api_reference/index
    maintenance
-
-.. toctree::
-   :maxdepth: 2
-   :hidden:
-   :caption: API
-
-   code-solv
-   code-msaf
-   code-sas
-   code-opt
-   code-utio
-   code-cli
diff --git a/docs/user_guide/changelog.rst b/docs/user_guide/changelog.rst
@@ -0,0 +1 @@
+.. include:: ../../CHANGELOG.rst
diff --git a/docs/cli.rst → docs/user_guide/cli.rst b/docs/cli.rst → docs/user_guide/cli.rst
diff --git a/docs/cpu_and_ram.rst → docs/user_guide/cpu_and_ram.rst b/docs/cpu_and_ram.rst → docs/user_guide/cpu_and_ram.rst
@@ -15,7 +15,7 @@ do some testing with regards to runtime, see the `Tools Section
 <https://emsig.github.io/emg3d-gallery/gallery/index.html#tools>`_. An
 example output of that script is shown in :numref:`Figure %s <runtime>`.
 
-.. figure:: _static/runtime.svg
+.. figure:: ../_static/runtime.svg
    :width: 80 %
    :align: center
    :alt: Runtime
@@ -94,7 +94,7 @@ do some testing with regards to the RAM usage, see the `Tools Section
 <https://emsig.github.io/emg3d-gallery/gallery/index.html#tools>`_. An
 example output of that script is shown in :numref:`Figure %s <ramusage>`.
 
-.. figure:: _static/RAM-Usage.svg
+.. figure:: ../_static/RAM-Usage.svg
    :width: 80 %
    :align: center
    :alt: RAM Usage

diff --git a/docs/user_guide/credits.rst b/docs/user_guide/credits.rst
@@ -0,0 +1 @@
+.. include:: ../../CREDITS.rst
diff --git a/docs/user_guide/index.rst b/docs/user_guide/index.rst
@@ -0,0 +1,18 @@
+.. _user-guide:
+
+==========
+User Guide
+==========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: User Guide
+
+   usage
+   mgwhat
+   theory
+   cpu_and_ram
+   cli
+   references
+   changelog
+   credits
diff --git a/docs/mgwhat.rst → docs/user_guide/mgwhat.rst b/docs/mgwhat.rst → docs/user_guide/mgwhat.rst
@@ -29,7 +29,7 @@ to the next node, and so on until it reaches the last node, see :numref:`Figure
 simultaneously per step (the fields on the boundaries are never computed, as
 they are assumed to be 0).
 
-.. figure:: _static/schematics2.svg
+.. figure:: ../_static/schematics2.svg
    :width: 60 %
    :align: center
    :alt: Explanation of smoother
@@ -64,7 +64,7 @@ The implemented multigrid method simply joins two adjacent cells to get from
 finer to coarser grids, see :numref:`Figure %s <fine2coarse>` for an example
 coarsening starting with a 16 cells by 16 cells grid.
 
-.. figure:: _static/schematics1.svg
+.. figure:: ../_static/schematics1.svg
    :width: 60 %
    :align: center
    :alt: Fine to coarse grid schematic
@@ -89,7 +89,7 @@ relaxation** :numref:`(Figure %s) <linerelaxation>`. Both require more CPU and
 higher RAM per grid than the standard multigrid, but they can improve the
 convergence rate, which then in turn improves the overall CPU time.
 
-.. figure:: _static/schematics4.svg
+.. figure:: ../_static/schematics4.svg
    :width: 60 %
    :align: center
    :alt: Schematic of semicoarsening
@@ -98,7 +98,7 @@ convergence rate, which then in turn improves the overall CPU time.
    Example of semicoarsening: The cell size is kept constant in one direction.
    The direction can be alternated between iterations.
 
-.. figure:: _static/schematics3.svg
+.. figure:: ../_static/schematics3.svg
    :width: 60 %
    :align: center
    :alt: Schematic of line relaxation

diff --git a/docs/references.rst → docs/user_guide/references.rst b/docs/references.rst → docs/user_guide/references.rst