Final RC (#216)

.github/workflows/linkcheck.yml

@@ -35,6 +35,4 @@ jobs:
 
       - name: Check links
         shell: bash -l {0}
-        run: |
-          cd docs
-          make html -b linkcheck
+        run: make html -b linkcheck

CHANGELOG.rst

@@ -9,7 +9,7 @@ Changelog
 Towards v1.0.0
 --------------
 
-- 2021-04-16: v1.0.0rc1
+- 2021-05-28: v1.0.0rc3
 
 There are _many_ changes, and they are listed below for each module.
 

Makefile

@@ -1,14 +1,15 @@
 help:
 	@echo "Commands:"
 	@echo ""
-	@echo "  install      install in editable mode"
-	@echo "  dev-install  install in editable mode with dev requirements"
-	@echo "  pytest       run the test suite and report coverage"
-	@echo "  flake8       style check with flake8"
-	@echo "  doc          build docs (update existing)"
-	@echo "  doc-clean    build docs (new, removing any existing)"
-	@echo "  linkcheck    check all links in docs"
-	@echo "  clean        clean up all generated files"
+	@echo "  install        install in editable mode"
+	@echo "  dev-install    install in editable mode with dev requirements"
+	@echo "  pytest         run the test suite and report coverage"
+	@echo "  flake8         style check with flake8"
+	@echo "  html           build docs (update existing)"
+	@echo "  html-clean     build docs (new, removing any existing)"
+	@echo "  preview        renders docs in Browser"
+	@echo "  linkcheck      check all links in docs"
+	@echo "  clean          clean up all generated files"
 	@echo ""
 
 install:
@@ -23,14 +24,17 @@ pytest:
 flake8:
 	flake8 docs/ setup.py emg3d/ tests/
 
-doc:
-	cd docs && make html && cd ..
+html:
+	cd docs && make html
 
-doc-clean:
-	cd docs && rm -rf api/emg3d* && rm -rf _build/ && make html && cd ..
+html-clean:
+	cd docs && rm -rf api/emg3d* && rm -rf _build/ && make html
+
+preview:
+	xdg-open docs/_build/html/index.html
 
 linkcheck:
-	cd docs && make html -b linkcheck && cd ..
+	cd docs && make linkcheck
 
 clean:
 	rm -rf build/ dist/ .eggs/ emg3d.egg-info/ emg3d/version.py  # build

docs/conf.py

@@ -38,7 +38,7 @@
     "numpy": ("https://numpy.org/doc/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
     "discretize": ("https://discretize.simpeg.xyz/en/main", None),
-    "empymod": ("https://empymod.readthedocs.io/en/stable", None),
+    "empymod": ("https://empymod.emsig.xyz/en/stable", None),
     "xarray": ("https://xarray.pydata.org/en/stable", None),
     "numba": ("https://numba.readthedocs.io/en/stable", None),
 }
@@ -108,4 +108,5 @@
 linkcheck_ignore = [
     'https://doi.org/10.1111/j.1365-246X.2010.04544.x',
     'https://doi.org/10.1088/0266-5611/24/3/034012',
+    'https://doi.org/10.1093/gji/ggab171',
 ]

docs/index.rst

@@ -51,7 +51,7 @@ emg3d Documentation
 
     +++
 
-    .. link-button:: https://emsig.xyz/emg3d-gallery
+    .. link-button:: https://emsig.xyz/emg3d-gallery/gallery
             :type: url
             :text: To the gallery
             :classes: btn-block btn-info stretched-link

docs/manual/cli.rst

@@ -14,8 +14,9 @@ default configuration filename is ``emg3d.cfg``, but another name can be
 provided as first positional argument to ``emg3d``. Note that arguments
 provided in the command line overwrite the settings in the configuration file.
 
-For an example see
-https://emsig.xyz/emg3d-gallery/gallery/tutorials/cli.html>`_ in the gallery.
+For an example see the
+`CLI example <https://emsig.xyz/emg3d-gallery/gallery/tutorials/cli.html>`_ in
+ the gallery.
 
 
 Format of the config file

docs/manual/references.rst

@@ -34,7 +34,7 @@ References
    <https://doi.org/10.1111/j.1365-2478.2006.00558.x>`_.
 .. [Muld07] Mulder, W. A., 2007, A robust solver for CSEM modelling on
    stretched grids: EAGE Technical Program Expanded Abstracts, D036;
-   DOI `10.3997/2214-4609.201401567
+   DOI: `10.3997/2214-4609.201401567
    <https://doi.org/10.3997/2214-4609.201401567>`_.
 .. [Muld08] Mulder, W. A., 2008, Geophysical modelling of 3D electromagnetic
    diffusion with multigrid: Computing and Visualization in Science, 11,
@@ -68,8 +68,8 @@ References
    DOI: `10.21105/joss.01463 <https://doi.org/10.21105/joss.01463>`_.
 .. [WeMS21] Werthmüller, D., W. A. Mulder, and E. C. Slob, 2021, Fast Fourier
    transformation of electromagnetic data for computationally expensive
-   kernels: Submitted to Geophysical Journal International;
-   `github.com/emsig/article-TDEM <https://github.com/emsig/article-TDEM>`_.
+   kernels: Geophysical Journal International, ggab171; DOI:
+   `10.1093/gji/ggab171 <https://doi.org/10.1093/gji/ggab171>`_.
 .. [Wess91] Wesseling, P., 1991, An introduction to multigrid methods: John
    Wiley & Sons. Pure and Applied Mathematics; ISBN: 0-471-93083-0.
 .. [WiMS10] Wirianto, M., W. A. Mulder, and E. C. Slob, 2010, A feasibility

docs/manual/usage.rst

@@ -18,9 +18,9 @@ Basic Example
 -------------
 
 The following is a *very* basic example. To see some more realistic models have
-a look at the `gallery <https://emsig.xyz/emg3d-gallery>`_. First, we load
-``emg3d``, ``numpy``, and ``matplotlib``. Note that this example requires that
-you have installed ``discretize`` and ``xarray`` as well.
+a look at the `gallery <https://emsig.xyz/emg3d-gallery/gallery>`_. First, we
+load ``emg3d``, ``numpy``, and ``matplotlib``. Note that this example requires
+that you have installed ``discretize`` and ``xarray`` as well.
 
 .. ipython::