Dev 1.0 (#212)

* Remove all backwards incomp. stuff (#186)

* Improve Survey (#187)

- Survey:
  - `frequencies` is also a dict.
  - Sources and receivers must be tuples or dicts; NO lists.
  - `name` is optional (and keyword only).
  - Optional `info` and `date` parameters.
  - No `Survey.observed`-attribute any longer.
  - No more `fixed` surveys.
  - `noise_floor` and `relative_error` are new stored as data array if they
    are not floats.
  - `data` can be a dict containing many data set.

- Dipole
  - No `name` any longer.

- Simulation:
  - `name` is optional (and keyword only).
  - Optional `info` parameter.

* Sphinx theme (#188)

* Re-work Core (#189)

* Re-work Solver (#190)

Solver:
* Start solver overhaul
* solve() does not take grid any longer; new signature, new `plain`
* New verbosity levels

Other
* Model is aware of grid; reduced TensorMesh
* _Map -> BaseMap
* _TensorMesh -> BaseMesh
* Field knows its grid (#191)

Documentation:
* Lots of documentation adjustements
* IPython and matplotlib sphinx-directives (#192)

* Re-work Model (#194)

- Not set properties (`property_y`, `property_z`, `mu_r`, `epsilon_r`) all return None if called.
- Not set properties cannot be set later.
- `model.case` are strings instead of numbers: `['isotropic', 'HTI', 'VTI', 'triaxial']

* Separate API docs per module (#195)

* Re-work Maps (#196)

* Rework entire interpolation stuff
* Cleaned-up maps

* Re-work meshes (#197)

* PEC to prolongation (#198)

* Re-work Fields Part I (#199)

* Remove SourceField
* Fields is not a subclassed ndarray any longer
* Inherit discretize conditionally
* Add setup.cfg for F401 on __init__
* Fix bug src-dep gridding in Simulation
* Do not (de-)serialize Maps

* Rework fields (#200)

* Cleaned module fields
* Add Win/MacOs; Python 3.9
* New fct emg3d.solver.solve_source
* New module electrodes; includes electric wire source

* Fix windows pytest failure (#202)

`pytest test_fields.py::TestGetReceiver::test_basics` fails on Windows, most likely with `emg3d.construct_mesh` - No idea why (`int32` issue?).

* Re-work electrodes (#203)

* Rework Surveys, Simulations, Optimize (#204)

* Magnetic field lives on faces again
* Outsource gallery again
* Do not store sfield, simplify rfield
* Add 'relative' to receivers
* New electrode convenience fcts
* Enable relative receivers in Survey/Simulation
* magnetic field use volume avg for mu again
* Simulation; no more grid
* to emsig.xyz and emg3d.emsig.xyz
* dict instead of tuples possible for construct_mesh

* Rework CLI/utils/io (#205)

* Rework io, utils, time
* master->main
* Move Fourier to new module `time`

* Fixes and docs for rc1 (#207)

* Improve docs
* Script to update old file format
* Fix rel. receivers in Simulation class

* Fixes to v1.0.0-rc.1 (#209)

- Fix adding noise to observed data in simulation if noise_floor is an xarray (related to point below) 
- Improve `survey.{noise_floor;relative_error}`

* fix workflow sed

* Further improvements towards 1.0 (#211)

* Further pep8 names in `core`
* Change discretize from master to main
* Re-enable `sphinx.ext.viewcode`
* Shorten doc urls (manual/api/dev)
* `max_prime` to `max_lowest` in `good_mg_cell_nr`
* Add CPU/RAM script to doc
* Fix fields.interpolate
* Update logo

.github/workflows/linkcheck.yml

@@ -12,9 +12,9 @@ jobs:
 
     steps:
 
-      # Cancel any previous run of the test job; [pin v0.6.0]
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@ce177499ccf9fd2aded3b0426c97e5434c2e8a73
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
         with:
           access_token: ${{ github.token }}
 

.github/workflows/pytest.yml → .github/workflows/linux.yml

@@ -1,11 +1,11 @@
-name: pytest
+name: linux
 
-# Only build PRs, the master branch, and releases.
+# Only build PRs, the main branch, and releases.
 on:
   pull_request:
   push:
     branches:
-      - master
+      - main
   release:
     types:
       - published
@@ -44,11 +44,15 @@ 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
             conda: "xarray tqdm empymod h5py scooby discretize matplotlib"
+          - python-version: 3.9
+            name: plain
+            os: ubuntu
+            conda: ""
 
     env:
       # Used to for coveralls flag
@@ -57,9 +61,9 @@ jobs:
 
     steps:
 
-      # Cancel any previous run of the test job; [pin v0.6.0]
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@ce177499ccf9fd2aded3b0426c97e5434c2e8a73
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
         with:
           access_token: ${{ github.token }}
 
@@ -81,8 +85,8 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup miniconda
-        # [pin master Feb 8, 2001]
-        uses: conda-incubator/setup-miniconda@77b16ed746da28724c61e1f1ad23395a4b695ef5
+        # [pin v2.1.1 (2021-04-01)]
+        uses: conda-incubator/setup-miniconda@35d1405e78aa3f784fe3ce9a2eb378d5eeb62169
         with:
           auto-update-conda: true
           miniconda-version: "latest"
@@ -132,8 +136,8 @@ jobs:
     needs: test
     name: Deploy to PyPI
     runs-on: ubuntu-latest
-    # Only from the origin repository, not forks; only master and tags.
-    if: github.repository_owner == 'emsig' && (github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/'))
+    # Only from the origin repository, not forks; only main and tags.
+    if: github.repository_owner == 'emsig' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/'))
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE
@@ -165,12 +169,12 @@ jobs:
           pip install -r requirements-dev.txt
 
       - name: Build source and wheel distributions
-        if: github.ref == 'refs/heads/master'
+        if: github.ref == 'refs/heads/main'
         run: |
           # Change setuptools-scm local_scheme to "no-local-version" so the
           # local part of the version isn't included, making the version string
           # compatible with Test PyPI.
-          sed --in-place "s/'root'/'local_scheme':'no-local-version','root'/g" setup.py
+          sed --in-place 's/"root"/"local_scheme":"no-local-version","root"/g' setup.py
 
       - name: Build source and wheel distributions
         run: |

.github/workflows/macos_windows.yml

@@ -0,0 +1,86 @@
+name: macos & windows
+
+# Only build PRs, the main branch, and releases.
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+# Use bash by default in all jobs
+defaults:
+  run:
+    # Using "-l {0}" is necessary for conda environments to be activated
+    # But this breaks on MacOS if using actions/setup-python:
+    # https://github.com/actions/setup-python/issues/132
+    shell: bash
+
+jobs:
+  test:
+
+    name: ${{ matrix.os }} py${{ matrix.python }}
+    runs-on: ${{ matrix.os }}-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos, windows]
+        python: [3.8, ]
+
+    steps:
+
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
+        with:
+          access_token: ${{ github.token }}
+
+      # Checks-out your repository under $GITHUB_WORKSPACE
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          # Need to fetch more than the last commit so that setuptools_scm can
+          # create the correct version string. If the number of commits since
+          # the last release is greater than this, the version still be wrong.
+          # Increase if necessary.
+          fetch-depth: 100
+          # The GitHub token is preserved by default but this job doesn't need
+          # to be able to push to GitHub.
+          persist-credentials: false
+
+      # Need the tags so that setuptools_scm can form a valid version number
+      - name: Fetch git tags
+        run: git fetch origin 'refs/tags/*:refs/tags/*'
+
+      - name: Setup miniconda
+        # [pin v2.1.1 (2021-04-01)]
+        uses: conda-incubator/setup-miniconda@35d1405e78aa3f784fe3ce9a2eb378d5eeb62169
+        with:
+          auto-update-conda: true
+          miniconda-version: "latest"
+          python-version: ${{ matrix.python }}
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          # The following should not be necessary with Mambaforg(?).
+          channels: conda-forge,defaults
+          channel-priority: strict
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --show-sources
+          conda config --show
+          conda install numpy pytest pytest-console-scripts pip
+          pip install setuptools_scm pytest-flake8
+          conda info -a
+          conda list
+
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          python setup.py install
+          pytest --flake8

.gitignore

@@ -3,7 +3,8 @@ __pycache__/
 
 # Sphinx
 docs/_build/
-docs/api/
+docs/api/emg3d*
+docs/savefig/
 
 # Pytest and coverage related
 htmlcov

.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: .