checking branch protection

.github/CONTRIBUTING.md

@@ -88,11 +88,20 @@ make test
 
 # Formatting
 
-Use the Makefile commands to locally format and check the code with `ruff`:
+Use the Makefile commands to locally format and check the code with `ruff` and
+`pylint`:
+
+```
+make style
+```
+
+This will run the following commands:
 
 ```
 make check
 make format
+make lint
+make pylint
 ```
 
 # Building docs

.github/workflows/ci.yml

@@ -1,21 +1,28 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
 name: CI
 
+# define when this workflow is triggered
 on:
   workflow_dispatch:
   pull_request:
   push:
     branches:
       - main
 
+# cancel any currently running workflows in this same PR
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-env:
-  FORCE_COLOR: 3
-  NUMBA_DISABLE_JIT: "1"
+# Use bash by default in all jobs
+defaults:
+  run:
+    shell: bash -el {0}
 
 jobs:
+  # run pre-commit which includes many formatting and linting tools
   pre-commit:
     name: Format
     runs-on: ubuntu-latest
@@ -33,12 +40,14 @@ jobs:
         run: |
           echo "::add-matcher::$GITHUB_WORKSPACE/.github/matchers/pylint.json"
           pipx run nox -s pylint
-
-  checks:
+  # Run tests and upload to codecov
+  test:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
     needs: [pre-commit]
     strategy:
+      # Otherwise, the workflow would stop if a single job fails. We want to
+      # run all of them to catch failures in different combinations.
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.11", "3.12"]
@@ -47,24 +56,46 @@ jobs:
         include:
           - python-version: pypy-3.9
             runs-on: ubuntu-latest
+    env:
+      FORCE_COLOR: 3
+      NUMBA_DISABLE_JIT: "1"
 
     steps:
-      - uses: actions/checkout@v4
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - name: Switch to Current Branch
+        run: git checkout ${{ env.BRANCH }}
+
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
         with:
+          activate-environment: invert4geom
+          environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
-          allow-prereleases: true
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
+          auto-activate-base: false
+
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: mamba list
 
-      - name: Install package
-        run: python -m pip install .[test]
+      # Install the package in editable mode
+      - name: Install local package
+        run: pip install -e .
 
-      - name: Test package
+      - name: Run the tests
         run: >-
-          python -m pytest -ra --cov --cov-report=xml --cov-report=term
-          --durations=20
+          pytest -ra --cov --cov-report=xml --cov-report=term --durations=20
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v3.1.4

.pre-commit-config.yaml

@@ -77,7 +77,7 @@ repos:
       - id: codespell
         name: codespell
         description: Checks for common misspellings in text files.
-        entry: codespell --skip="*.js,*.html,*.css,*.svg,*.ipynb"
+        entry: codespell --skip="*.js,*.html,*.css,*.svg,*.ipynb" -L ore
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
     rev: "v0.9.0.6"

Makefile

@@ -26,3 +26,8 @@ check:
 
 lint:
 	pre-commit run --all-files
+
+pylint:
+	pylint invert4geom
+
+style: format check lint pylint

README.md

@@ -24,8 +24,6 @@ tesseroids instead of prisms.
 See the [overview](overview.md) for further description of this package and what
 it can be used for.
 
-The tutorials
-
 <!-- prettier-ignore-start -->
 [actions-badge]:            https://github.com/mdtanker/invert4geom/workflows/CI/badge.svg
 [actions-link]:             https://github.com/mdtanker/invert4geom/actions

docs/citing.md

@@ -1 +1,5 @@
 # Citing Invert4geom
+
+```{warning}
+Citation info still to come ...
+```

docs/gallery/index.md

@@ -1 +1,5 @@
 # Gallery
+
+```{warning}
+Gallery examples still to come ...
+```

docs/install.md

@@ -1 +1,31 @@
 # Install
+
+```{warning}
+Install instructions still to come ...
+```
+
+For now, clone the GitHub repository and change directories into it:
+
+```
+git clone https://github.com/mdtanker/invert4geom.git
+cd invert4geom
+```
+
+assuming you have `Python` and `make` installed, as well as `mamba` (install
+mamba with `pip install mamba`) installed within your Python environment, run
+the following to install the package locally:
+
+```
+make create
+conda activate invert4geom
+make install
+```
+
+If you don't have or want `make` or `mamba` installed, you can accomplish the
+same with the following:
+
+```
+conda create --name invert4geom --yes --force antarctic-plots python=3.11
+conda activate invert4geom
+pip install -e .[viz,test,dev,docs]
+```

docs/overview.md

@@ -1 +1,25 @@
 # Overview
+
+Invert4geom provides a series of tools for conducting a specific style of
+gravity inversion. Many gravity inversions aim to model the density distribution
+of the subsurface. These are commonly used to identify bodies of anomalous
+densities, such as igneous intrusions or ore deposits. The typical way these are
+performed is to _discretize_ the subsurface into a series of finite volumes,
+such as cubes or prisms, where the shape of the volumes doesn't change. The
+inversion then alters the density values of each of these volumes to match the
+observed gravity anomaly. In these inversions the _density_ values changes,
+while the _geometry_ of the volumes remains unchanged. These types of inversions
+may be referred to as _density inversions_. Here, instead, we are performing
+_geometric inversions_.
+
+Geometric inversions are essentially the opposite. The density values of the
+volumes in the discretized model remain unchanged, while their geometry is
+altered. Here we use layers of vertical right-rectangular prisms and alter their
+_tops_ and _bottoms_ during the inversion. Typically use cases for these style
+of inversion are modeling the topography of the Moho, the contact between
+sediment and basement, or the shape of the seafloor in locations where it is not
+easily mapped.
+
+Currently, this package is only intended to perform inversions using right
+rectangular prisms. Other types of volumes, such as tesseroids, are currently
+not implemented.

environment.yml

@@ -0,0 +1,31 @@
+# Requirements for running the github action: test only need run-time dependencies
+name: invert4geom
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.8
+  - pip
+  # Run-time
+  - numpy
+  - pandas
+  - xarray
+  - verde>=1.8.0
+  - rioxarray
+  - pykdtree
+  - xrft
+  - harmonica>=0.6.0
+  - antarctic-plots
+  - numba
+  - scipy
+  - nptyping
+  # viz
+  - pyvista
+  - trame
+  - ipywidgets
+  - matplotlib
+  # test
+  - pytest >=6
+  - pytest-cov >=3
+  - pip:
+      - numba-progress

pyproject.toml

@@ -68,6 +68,7 @@ dev = [
   "ruff",
   "nox",
   "pre-commit",
+  "pylint",
 ]
 docs = [
   "sphinx>=4.0",

src/invert4geom/inversion.py

@@ -1,4 +1,4 @@
-from __future__ import annotations
+from __future__ import annotations  # pylint: disable=too-many-lines
 
 import copy
 import itertools

src/invert4geom/plotting.py

@@ -162,8 +162,8 @@ def plot_inversion_topo_results(
     for g in [initial_topo, final_topo]:
         topo_lims.append(ap_utils.get_min_max(g))
 
-    topo_min = min([i[0] for i in topo_lims]) * topo_cmap_perc
-    topo_max = max([i[1] for i in topo_lims]) * topo_cmap_perc
+    topo_min = min([i[0] for i in topo_lims]) * topo_cmap_perc  # pylint: disable=consider-using-generator
+    topo_max = max([i[1] for i in topo_lims]) * topo_cmap_perc  # pylint: disable=consider-using-generator
 
     # set figure parameters
     sub_width = 5
@@ -349,15 +349,15 @@ def plot_inversion_iteration_results(
     for g in corrections_grids:
         corrections_lims.append(ap_utils.get_min_max(g))
 
-    misfit_min = min([i[0] for i in misfit_lims])
-    misfit_max = max([i[1] for i in misfit_lims])
+    misfit_min = min([i[0] for i in misfit_lims])  # pylint: disable=consider-using-generator
+    misfit_max = max([i[1] for i in misfit_lims])  # pylint: disable=consider-using-generator
     misfit_lim = vd.maxabs(misfit_min, misfit_max) * misfit_cmap_perc
 
-    topo_min = min([i[0] for i in topo_lims]) * topo_cmap_perc
-    topo_max = max([i[1] for i in topo_lims]) * topo_cmap_perc
+    topo_min = min([i[0] for i in topo_lims]) * topo_cmap_perc  # pylint: disable=consider-using-generator
+    topo_max = max([i[1] for i in topo_lims]) * topo_cmap_perc  # pylint: disable=consider-using-generator
 
-    corrections_min = min([i[0] for i in corrections_lims])
-    corrections_max = max([i[1] for i in corrections_lims])
+    corrections_min = min([i[0] for i in corrections_lims])  # pylint: disable=consider-using-generator
+    corrections_max = max([i[1] for i in corrections_lims])  # pylint: disable=consider-using-generator
     corrections_lim = (
         vd.maxabs(corrections_min, corrections_max) * corrections_cmap_perc
     )
@@ -729,7 +729,7 @@ def show_prism_layers(
         plotter.camera.zoom(kwargs.get("zoom", 1.2))
 
     # Add a ceiling light
-    add_light(plotter, prisms[i])
+    add_light(plotter, prisms[i])  # pylint: disable=undefined-loop-variable
 
     plotter.show_axes()
 

src/invert4geom/synthetic.py

@@ -78,7 +78,7 @@ def synthetic_topography_simple(
         pixel_register = True
 
     # create grid of coordinates
-    (x, y) = vd.grid_coordinates(
+    (x, y) = vd.grid_coordinates(  # pylint: disable=unbalanced-tuple-unpacking
         region=region,
         spacing=spacing,
         pixel_register=pixel_register,